Can you say more about how you got into this situation? I was unable to replicate. So far I tried these situations:
* have a stack of units that are all in patrol mode, next turn select 2 units to activate, move them to a nearby square. works fine
* have a stack of units that are all in patrol mode. have another stack nearby that is active walk a path through the patrol stack. the non-patrol units walk through the patrol units just fine and have the expected number of movement points