Okay so I am on Skybird Trill and I have managed to capture and convert the Avatar leaving only the blue dungeon to deal with however for some reason even when I destroy the dungeon heart the level complete message does not trigger. I think the level might be bugged or something. Has anyone else ran into this issue

Killing the blue dungeon is not the end of the level. There will be one more final battle that pops up shortly after killing the blue dungeon. I'm not sure if the white dungeon in the middle needs to be killed, but the blue guys usually kill it for me anyways.

Turns out there was a group of heroes I somehow missed completely. They apparantly got stuck attempting to tunnel in. I took care of em and it was basically level complete which is weird since with the Keeper FX version of Skybird Trill you are expected to destroy the enemy dungeon in addition to dealing with the Avatar

It might be the case that you are on KeeperFX Unofficial, which restored, among other things, the original victory condition of the final level. It does include the New Game+ campaign, which is basically the same campaign again but without it being one big tutorial, and that does require you to finish off the blue keeper at the end.