It seems like 75% of preppers are pro-bugging in once the SHTF. When deciding to bug in or bug out, there is one crucial question that you need to ask: 'Will society collapse?' If society won't collapse, bugging in is probably fine. If society will collapse, bugging in would be stupid. Here's why:
Your neighbors and other refugees who haven't prepared with stored food will be knocking at your door to see if you're home and if you can help them with food and other needs. Perhaps your neighbors will be aware that you are there and eating, making it all the more difficult to turn them away. You will basically have to watch some of your neighbors starve to death. Can you deal with that? How will you handle that situation when you start seeing people looking like they just came out of Auschwitz?
Once food runs out, people will get desperate and do whatever they have to to eat and survive. If you bug in, there is a good chance that some thieves will attempt to rob your house. If you have good defenses and are ready to use your guns, you can probably scare them away or successfully defend your home, but do you want to risk it? Plus, once they've engaged you and realize people are living in that home, when they get really really desperate, they might return, since they think there is a possibility you have food.
Even worse than regular thieves will be street gangs, cartels, prison gangs, and warlords that rise up. It will only take a couple weeks for these groups to organize and rise to power. One of their primary focuses will be storing up food. I imagine they will systematically sweep neighborhoods by going house to house with trucks and a dozen armed men. They will get to your house eventually. Especially if vehicles are still running, I imagine every single house will get hit by thieves and gangs multiple times. It will happen. It's just a matter of when. Will you hide or attempt to fight them off? Remember, this time it's not just 2 or 3, it's 10-20. Do you want to risk it? If you make the choice to bug in in a collapse scenario, this is a risk you are taking. Also, the cold hard reality is that these guys are thugs who might take any attractive women and girls as sex slaves. Are you willing to risk having your wife and daughters as sex slaves if you fail to defend your home? Many preppers have a plan on destroying the entrance and part of the home to make it look like raiders have already been there and looted the home. This is probably a good idea, but if you do that, you're forced to live in a broke down house. Will that be fun?
When the collapse happens, you might get transformers and other machinery exploding and causing fires. Also, riots will start fires and people cooking with open flame will cause accidents and start fires. Firefighters have already left their posts, since they are more concerned with the survival of their families, so no one will be left to put out the fires. Fires will rage through cities. If you live on an upper floor of a tall building, you have even more to fear. Fire threats make bugging in really dangerous. (Your best counter to this threat could be having an air tight under ground bunker to jump in when the fires come.)
5) WATER ISSUES
Water will stop running out of the faucet. Storing up water is great, but what happens when you run out? You can harvest water, but does it rain enough to water your garden, give you drinking water, and washing water? If not, you will have to deal with feeling dirty and gross all the time, getting fungus, having body odor, and perhaps being thirsty and having a struggling garden. If there is a source of water nearby where you will fetch water, it probably won't be safe to travel there and back. Making yourself visible is always dangerous, even if it's just crossing the street.
6) FOOD ISSUES
Obviously you will want to store up food. But once your food runs out, you will need to start gardening, raising food, or hunting and foraging. What's the point of bugging in if you will eventually need to leave to find a place to farm? Why not go and secure a piece of land where you can farm right away? It doesn't make sense to wait, because it will be like starting over. If you bug in for 10 years with the 10 years of food you have stored up, you will be at level 0 once that food runs out, while the other survivors will have flourishing farms and trade networks set up already. Growing a garden in your backyard can be done if you make really good use of the space, but if neighbors and thieves peak over and see the Hanging Gardens of Babylon in your backyard, which will basically be what you'll need in order to feed your whole family, you will make yourself a big target. It is a big risk being seen with all that food. Furthermore, you will need to spend a lot of time out there tending to your garden. You'll make some noise and might be seen. You would be better off clearing a little patch of land in the middle of the forest where no one will ever find you. Also, if you have years worth of food stored up, you will need to realize that there is always the possibility that someone might steal it. Hidden storage and caches are helpful, but you might be run out of your house completely. No matter how bad a** you are, you can't entirely rule out the possibility of being run over. Or what if you realize that it has gotten so dangerous that you need to bug out and now the roads are blocked and you won't be able to bring all the food with you as you bug out on foot? If you plan on bugging in and still eating meat, it will be extremely difficult. Tilapia will probably be your best bet, but water might be scarce. Rabbits are great, but they will require a lot of extra grass to be grown or you will have to go out in public to fetch the naturally grown grass. Chickens are noisy. Raising insects might work. Catching birds, squirrels, and dogs might also work.
7) FUEL ISSUES
You will need to cook your food and perhaps have a fire to stay warm and boil water. Propane is a start and having firewood stocked up is a start, but again...what happens when that runs out? Remember, the collapse is total and complete. Society can't just reboot itself in a year or two. Can you collect wood nearby to burn? Other survivors will be trying to do the same, so is there enough firewood for all the survivors? Also, every time you go outside, you expose yourself to potential crime or stalkers who will follow you home and steal from you there.
8) SANITATION ISSUES
This piggy backs off the water issue. Is there enough water to bathe and wash your clothes? There probably won't be if you are only harvesting water from your roof. The other big issue is what do you do with your waste? The sewers aren't flowing and the garbage men aren't picking up the trash. If you have a septic tank, you're lucky, but most will need to dig an outhouse. Also, have you stored up enough soap? What will you do once you run out of soap? Do you have plans to make your own soap? Toothpaste? Deodorant? From what I understand, it will be easier to make these things on a farm with animal oils/fats and more room for production.
9) NOISE ISSUES
Because of the fear of being caught alive and well by the wrong people, you will be cautious about making noise. You can't talk loudly, laugh out loud, sing, play games, and be yourself. Perhaps you could in a basement or bunker, but it will be difficult trying to be quiet all the time, especially when you need to build and construct things.
10) FIRE & SMOKE ISSUES
Cooking food and boiling water means that you will have fire and smoke. Fire and smoke can be a sign to the bad guys (or even your neighbors) that people are alive and perhaps cooking. Cooking inside is better so you can maintain a low profile, but there will still be smoke coming out your chimney. However, this is one instance where the city fires can help you. If there is already a lot of smoke in the sky, your small fire will not cause much of a problem. In terms of using less wood and emitting less smoke, rocket stoves are good, fan assisted stoves are better, solar ovens and fresnel lenses are the best, but these last two will require being outside during the day.
11) LIGHTING ISSUES
At night you will have to be weary of having any lights on or flames showing to the outside world. Even a glow can catch someone's eye. You will need to use dark curtains if you want to have lights on at night. Or you could designate a couple inner rooms as the ones to use at night to lessen the chances of light exposure to the outside world. If you were to bug out instead, you can use flashlights, lanterns, and campfires as much as you want at night. If you bug out to a remote forested place, the risk of being discovered by bad guys will be so low that you wouldn't have to worry too much, especially if you take a few easy precautions.
12) PERMANENT STINK
You might stink. Others in your group might stink. Your clothes might stink. Your dirty towels might stink. Your outhouse might stink. The whole town will stink from garbage, rotting bodies, sewage backup, etc. It will be gross. You will begin to hate it. If you bug out to the wilderness, you'll have plenty of fresh air and water to wash all you want.
13) PSYCHOLOGICAL PROBLEMS
All of the above issues will begin to wear you down and make you go crazy. You are confined to your home. You see your neighbors starve. You are afraid to be seen. You have to keep quiet all the time. You are paranoid that every noise outside is gangsters coming to kill you and take all that you have, so you don't sleep well. You can never relax. It stinks real bad. You get cabin fever. You want to go for a walk just to get out of the house, but you can't. The stored up food is starting to taste nasty. There is smoke in the air all the time. You aren't getting along well with your family and the kids are crying often. Bugging in will become a nightmare situation.