I accidentally shot Ian (a combat partner) from a distance while trying to shoot a rat. He shot back at me and wouldn't stop. Luckily I had a recent save to revert to. But, if this happens again is there any way to get him to realize he's on *my* side? I notice that when he's behind me and wants to shoot at something, his bullets seem to go right through me with no damage. Not the other way around, I guess. Thanks.

Unfortunatly not, just be careful when shooting at things and keep saving often.

General rule of thumb with Ian and other NPCs that join you is this:
Make sure they are nowhere near your line of sight on a target.
Try to have them standing beside you in a fight if possible.
Never stand in front of them because you will get shot in the back.

Well, that's strange, because a couple of times I was standing right in front of him and he shot right thru me. He hit the rat but I took no damage. Just lucky? I won't take any chances, though. Thanks.

Ha... well, I'll look over my shoulder then... :)
Thanks again.

Yep. You're welcome :-)