I just noticed this myself. Downloaded the windows release version a few days ago. If my soldier is crouching at the beginning of the turn and I find a square to move him to that uses all of his TUs(31), he uncrouches, walks over, crouches and still has 3 TUs left. The next turn, as an experiment, I uncrouched him manually, walked to the original spot and crouched. Again I had 3 TUs left. When I uncrouched my soldier, it said it would be 22 TUs to walk to the square. 3 + 22 + 3 = 28. So I think the algorithm to determine the TUs used to move while crouched is adding in an extra crouch. The algorithm when he isn't crouched is correct (as far as I could tell).
Autostand/Autocrouch was not on.
Beautiful game, BTW. A thousand times, thank you all.