Here's an example... You're on a trade run, and there is an Ion Storm in I-3 (Just trowing in sector here). When you go through it one way, it stops you like normal, but when you pass the other direction it doesn't affect you at all... I've run into a couple of these lately. I assume this is a bug?

It could be, or your return trip may coincide with the storm moving to another sector. If I experience that, I'll check the adjacent sectors.

Was it the only Ion Storm you got caught by in that system? I have had times that I've been caught in one storm ("A"), and the route from that storm to my destination hits a second storm ("B") that my initial route would not have encountered. Going back the other way, I would only be caught by one of the two storms, because "B" would not be directly on my route, and I would already be past "B" when I get caught by "A".

I can confirm this, this has happened to me more than once with the same storm.

This does occur, I had one in helios B-13 that would stop you if you were going from B-7 to B-14 but not when you went the other way. I tested it extensively the one day by jumping through it in both directions in a direct line repeatedly, and I think i submitted a bugreport on it, but now i cant remember for sure.