Seems to me that the update 3.0.3 finally fixed Fenris teleporting strikecrafts between them, nice work sir.
With that being said, it appears to me that strikecrafts are also more prone to landing on enemy carriers and never get promply rearmed ever since, especially with aleste series.
Also, even if the strikecrafts no longer rely on waypoints to rearm, they may still be locked in the land-takeoff-land cycle sometimes, and- weiredly- switching to other windows with the game unpaused seems to fix it somehow.
EDIT: Further notice that I'm also getting enemy Bakraid spawning friendly Panther glich in the Hegemony HVB, also- for further notice- I did not have a single Bakraid in my fleet