Carrier pets no longer following the carrier, this is a recent issue, they are also not docking again.
I have a solution to the not docking issue though given that this bug has been around for ages coming and going. Why not beam fighters aboard like in Nemesis, this would be faster and less problematic, perhaps to stop that being abused put a timer on it when you activate it they take 5 seconds to dock, it would still be faster than the current mess. As for frigate pets have them perhaps tractor beamed back, or have them all tractored back in, this would sort the issue out and would make sense that even normal ships tractor their shuttles aboard.
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