I've now seen it a couple of times where units moving through other friendy units (as now allowed in 1.1) can end their movement on the same tile as the friendly units. I assume this is not intended. Not sure what would happen if the AI attacked that square, that's not happened yet.
While it's not possible to deliberately select a friendly unit as your target for movement, what I think is happening is that I click on an enemy unit to attack and my unit moves as far as it can go, which happens to end on the same tile as another friendly unit.
If that's what's happening than one fix would be to not allow units to enter a tile with a friendly unit unless it has at 2 movement points left (i.e. it won't run out of movement points on the tile of the friendly unit).