There is a scripted encounter I've run into a few times now. You find a Mantis ship in a mantis sector and when you do enough damage they make a hasty retreat. You can follow them to find they are now in a bigger ship than before. Thats all fine, but how did they escape when I had a boarding party in their cockpit and they were about 1 second away from killing the pilot. Theres no way that should have been possible. So They escape somehow and I follow them to find my crew is not on the new ship. This is frustrating. The time between the dialog box saying they were trying to escape, to them actually FTL jumping away was only 1-2 seconds.
The weird thing is once you scare away the new bigger ship(or perhaps destroy it) you get a whole lot of scrap from their abandoned ship that my crew should have been on.