That could be two things. Yes, it will tend to level to just below a wooden tile if you're standing on one. This doesn't usually leave a visible gap however, and may be the issue of leveling only raising so far - I suggest raising this bit of ground and trying to level it again, see if that works. Either way snapping a wooden stairs onto the edge of that wooden floor tile should get you a smooth transition for the cart.

It's also not infinitely variable, such that it is possible to get a mismatch where no matter what you do building pieces and terrain just won't play ball.