Hmm, we had changed the behavior of wormholes to be blocked if they are covered by enemy forcefields even if you can get physically over to them -- this prevented things that move incredibly fast (or are on fast forward) from sneaking through covered wormholes. It sounds like that new(ish -- a few months old) code is what you're running into.
I didn't remember that crippled flagships were set to be able to go through AI forcefields. If that's the case and what the design says (that was a year ago when I was working on that bit probably), then I can make it so they are the exception to the wormhole-coverage check. There are some newer units that are able to move through enemy forcefields in general, and they probably still get caught by the wormhole traversal logic like your stuff does.
Definitely worth a mantis!
