Ok, so for some reason, though it says i can add certain additions like Alchemy Laboratory, Enchanting Tower, Bedrooms, etc.

And when i do, the additions don't appear on my house, even though the game says they were added.

I know i did click on some of those options, more then once, could that have caused the additions to not appear? Or will they, but it will take time?

Assuming these are the first three additions your putting on the house, they should show up in a short period of time. If these are the 4th, 5th and 6th additions, then no, you only get 3 total, plus the basemant.

Did you have the materials to build these additions?

Did you actually build any of them, or were you still in the planning stage? You choose one addition and go to the other table and build it, then choose what you want for the other two wings. You choose something else at the planning stage, it just cancels what your previous choice was.