Hi @LizRivera,
Probably there is some inaccuracy in your geometry. I slight inaccuracy in the z-direction is enough to cause this problem. The best way to solve this, is to draw your plans just as simple 2d line drawings and put each level in a different block. You can import these blocks in grasshopper with the Human pluginn.
.
For the plans I use three layers zo I can sort out innerewalls, outerwalls and windows. From the outer wall I generate a floor surface which can be split by the innerwalls. The different surfaces now can be extruded.
The advantage of using blocks is that you can put them on different places in the drawing. So you can make one set for the energy model (put on a the layer for the energy model) and one set on the ground plane, where you can change the layout (put on a different layer). This will avoid small Z-inaccuracies