To clarify how warp bubbles and similar fleet-speed-enhancing (FSE) modules work:
If the ship is by itself, it will get the speed bonus + its base speed.
If the ship is in a fleet, the best FSE module in the fleet becomes the active FSE ship. The movement points for this ship are ignored when calculating the fleet speed. So, the fleet's moves will be based off of the ship with the least moves in the fleet (not counting the active FSE ship) plus the FSE bonus.
For example:
Ship A ( 4 moves )
Ship B ( 2 moves + 1 FSE )
Ship C ( 5 moves )
Ship D ( 1 move + 2 FSE )
If all of these ships are fleeted together, the fleet would have 4 moves. This is because ship D has the highest FSE bonus, so it is not considered when getting the ship with the least moves. The ship with the least moves is Ship B with 2 moves. Even though it has 1 FSE, this does not matter because the FSE is not active. So the fleet will move 4 moves. This is 2 moves (slowest ship) + 2 FSE (from active FSE ship D)
As soon as you remove ship D (or ship D is killed in battle), the fleet will have 5 moves. This is because the active FSE ship is now ship B so it is not considered for the least amt of moves. The slowest ship now is Ship A which has 4 moves. The fleet gets 4 moves (slowest ship) + 1 move (from active FSE ship A) for a total of 5 moves.
This is the intended behavior. If you notice this is not happening, please let us know.