I'm enjoying the game. I think I played the first one too while I was stuck with only a laptop for a while. I look forward to seeing how the development goes.
I checked the patch notes for 0.6.0 and it sounds like you took a stab at the units and their models getting misaligned. It seems that the problem persists. I have been saving and reloading the matches to fix it. For me, it seems that the misalignments happen when moving a unit as far as they can go in one turn.
Edit: Another bug - Units that are stored in a helicopter can switch teams if they are in the style of the enemy and the game is saved, then reloaded. They are in an in-between state when first dropped, their icons in the bottom left corner are the enemy team color, but they cannot be attacked. Upon the enemy's turn beginning, they then begin to attack (likely the helicopter that just dropped them off).
I had to quit a mission because of that. I frequently save and reload so that I can see where units actually are, but after my only veteran helicopter was destroyed by the unit it just dropped off... I needed a break. Best of luck finding the bug!