Change your target attack profile. Instead of targeting the manned bomber (lead) first, go for the one either port or starboard of the lead bomber. This way when you do blow it up, it won't warp like the lead bomber does and cause a collision. On your 2nd pass (after you've killed either the port or starboard drone) then you can safely attack the lead bomber as the remaining drone (when the player jumps into it) won't warp to the lead position since the are no other bombers to form up on.
ack-ack
Adjusting your attack or target order of buff groups to ensure the safest passes from guns is one thing. Adjusting the target order or path of attack to also dodge a warp is a valid point.
I hate when we so quickly dismiss the real issue with responses like, "just change how you do things." In the end that may infact be what is needed, but exploring the OP's observations through discussion may also lead to solutions.