When in a Corpus Railjack mission, after the initial objectives have been completed and you are able to enter the capital ship, if you enter the ship via the slingshot, the mission instantly fails. Entering the capital ship normally does not trigger the mission failure. Slingshot into a crewship does not trigger mission failure.
Other details:
Playing on Xbox Series X
Playing as Nekros with the Amesha archwing
Tested in Venus Proxima
Tested in fissure survival mission (first noticed), regular survival, and regular exterminate