Hmm are you sure you are putting them exactly as the blueprint says? there are only a few types of buildings that need to be in a specific location (those that go near water or rock outcropping); most buildings can go anywhere.
Once you put the first piece of a building down, when you are carrying another piece of the building it will have a cyan (light blue) square where you need to put it in relation to the first piece. Repeat for next piece, etc. Once all pieces are in place it should build automagically.
Hope this helps. Post back with more details if not.
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