At that point, I had three engine upgrades (to level 4) and Long-ranged scanners instead of the Mantis pheromones.
As I have experienced the shuttle message several times before with no instant game over screen, I have no clue what caused the game to trigger the false loss message this time.
Update: after looking some more at the screenshot, I have a strong hypothesis: the second small bomb destroying my cockpit was just fired before the last enemy crew was killed, and the shuttle that returns your crew when your teleporter has been destroyed unloads everyone (instantly) into the cockpit, so the small bomb killed both my returned Mantis in the cockpit... so the bug/issue is that the crew is instantly returned by shuttle, so the shuttle is even faster than a teleporter would have been.
Here the screen shot:
