When you select a part, it turns blue (or green or orange) but that's not only what happens, if you check closer you'll see, that ther is a orange wireframe cube around it, and that's it, that's why your floor looks below the part.
First you see this:
The solution is simple: locate the wheel missaligned (maybe all of them are missaligned) and do what you shouldn't do in regular conditions, add unnecesary mates
Now you're wheels are aligned
The box is aligned:
And your floor is fine: