That certainly looks like an acid issue,if thats metal showing..
I think I'd toss that rust mort and either use Ospho or nothing at all..
Did you epoxy then use the filler on top of that or filler to the metal?
The thickness of the material is one of the main reasons I hate 2k primer,once you guide coat it and get it straight most people stop right there but theres still a ton of material on there that doesnt need to be there,causing thick,nasty lookin chips and cracking in some cases,door edges especially...
I think I'd try getting a razor blade in there between the metal and whatever that is and trying to scrape it off until it sticks..It should scrape right off,at least down as far as it starts sticking again ...is that happening anywhere on the rest of the car?