1. You’re not building your vault efficiently.
There is only one layout that maximizes the efficiency and cost-effectiveness of your entire vault. By now you should know it is better to merge rooms before you upgrade them. You get more production/storage per cap that you spend when you upgrade a double or a triple room as opposed to just a single.
What this also infers is that you should only have two straight columns of elevators. Every floor minus the top floor with the vault door should have the following rooms (in whatever order you happen to building your layout): two triple rooms, a double, and two elevators. I like having the first elevator aligned right beside the vault door and the second elevator to the far right against the dirt; this lets you swap around the double and triple room to make it look a bit nicer.
2. You have a radio station.
But seriously, the radio station only does three things, two of which are bad. The only good thing it does is boost the happiness level of your dwellers, but this is completely useless. Happiness only translates to caps at the end of your daily report, and you only get around 120-140 caps. The second thing it does is attract dwellers. This is bad because you only get level one dwellers with base stats via the radio station. If you get a raging hard-on for level one dwellers, you’re better off forcing your existing dwellers to mate; it’s way faster and you’re literally spreading the love. The last thing, of course, is that radio stations instigate Deathclaw attacks, and there is no good reason to want this.
3. You’re not renovating.
When you get to 100 dwellers you’ll unlock the Nuka-Cola Bottler, the last room. You’ll also have the Nuclear Reactor, Garden, and Water Purification Station. At this point you should be destroying your tier-1 resource rooms. The tier-2 rooms provide more resources and capacity, and it’s better for your now higher level dwellers to be matched with higher level rooms, for efficiency’s sake.
Depending on if you’re playing on your phone and how deep you want to take your vault, this may also help with lag issues. Fewer rooms producing more resources is better than more rooms producing the same amount of resources. Renovating also lets you clear away the terrible choices you made when you first started playing, and also the initial Living Quarters that the game forces you to build right next to the Vault Door. Since that room is where Raiders and Deathclaws go to first, it makes sense to build a room where your higher level dwellers will spend the most time.
The above screenshot is what my vault looks like as I write this. Yes, I have a single room, but it’s a training room so it doesn’t effect resources. At the point where I am (105 dwellers), I’m only concerned with training rooms. Caps don’t matter to me as much as getting my dwellers ready to go out exploring. The blank space is where I recently destroyed my Diners and Water Treatment Stations to be replaced with more training rooms.
4. You’re not saving your equipment.
Don’t sell all your weapons and outfits immediately. You want every dweller to have a weapon. Random incidents can happen anywhere, and your first Deathclaw attack will have you wishing every dweller was equipped with something. When you begin exploring the wastelands more, you’ll bring back stronger weapons. That’s when you should start selling your weapons that do 1-3 damage, so long as you can replace them with sawed-off shotguns. Outfits with +3 in any one stat are also useful because you never know where you’ll rearrange what your dwellers are doing, and a +3 for the relevant SPECIAL is very useful for whatever production room you end up throwing your dwellers in.
5. You’re not building enough training rooms.
This should be your priority. The best way to collect caps, weapons, and outfits is by sending dwellers to explore the wastelands. Dwellers with high SPECIALs have a greater chance of surviving, and the longer they’re out there the greater chance they have at finding rare loot. A high luck rating helps directly with that, which is why I built multiple Game Rooms first.
This also contributes to the overall efficiency of your entire vault. Having more dwellers with higher SPECIALs will lessen the time it takes to produce resources, which means less resource-producing rooms are required. This will let you build more training rooms, Medbays, and Science Labs (higher capacity for Stimpaks and RadAways means you can send more dwellers to the wastelands faster).