You don't need refuel routines for vehicles. They will refuel automatically if they are below the threshold (about 20% I think) and passing a fuel station or barrels.
I know the problem you refer to: never got to the bottom of it myself but I think it's a randomness thing. OFP has randomness built into it, that's partly what makes it such a great game. Let it run for long enough though, and the bizarre, crap very unliklely possibilities come home to roost.
The lead vehicle is indeed rarely the one to hit trouble: I think this is because it has a clear road with nothing to do but follow waypoints. The other vehicles have to follow the leader. Because of the random element, the leader will take a slightly different route down the same stretch of road each time. Because of the random element, the other vehicle will follow in a slightly different way each time. If you run the simulation enough times, sooner or later the other vehicle will get itself stuck between two trees.
The solution, I think, is a slow loop that checks the position of each vehicle. If it hasn't changed, and it is supposed to, then setpos it a few yards away. At the end of the setpos section of the script I'd refuel and repair the whole group, just to be on the safe side. If you want to be sure the player doesn't see, check that he is sufficiently far enough away.
I ignored all this in the Un-Finishable Mission because it didn't really matter: I had repair routines to keep them on the road but the blackop motorbike patrol, for example, rarely makes it round its loop even once without coming to grief. However, this just splits the group up which in some ways adds to gameplay - you never quite know if you've got them all.
Edit: Armsty is right.