If you're trying to place a building on a lot that won't accept it, there are a couple reasons why that could be.
If you're sure the lot is large enough, and its set to commercial, then maybe there is a rock or gem or insect spawner stuck on the lot that you cannot see. What I do is go into buy/build mode, draw a wall on the lot, then exit back to map view and use the bulldozer to delete the contents of the lot. Only delete once so you don't remove the lot itself.
Then try to place your wanted building on the lot and see if it works.