I'm also stuck on two betrayals, right before "destroy mcmuffin #3". The banshee won't let me board, so I made a hoverhog from a d20 instead ... but once up there, there's no enemies or even a generator present. The waypoint also stays stuck on the door.

Maybe could be related since it's the same level?

this is just the way vanilla two betrayals is, you just have even more tools to skip a mission trigger with in cursed halo

So, I think i've figured this out. Apparently the game detects whether or not you're in a Banshee when it comes to spawning enemies and moving the waypoint when you get up there, so being in a hoverhog from a d20 won't work.
I also had the issue of the banshee before the third generator not letting me enter it. However, if you go further down the path, there's a pretty well defended area with 2 completely vacant Banshee's that CAN be entered. Bringing one of those back worked for me

Try not to fly over mission triggers or else the game will stop spawning enemies and not allow you to progress past certain points unless you go back and activate the triggers.