Yes, absolutely correct. You need to destroy the big ship. Then “find” the small one (on Lapine it’s not so important, but for stronger opponents this may become tricky), tie up the opponent and finish the small ship.
Ughmm… this is intended behavior :) You need to win with the opponent tied up to capture her. Or maybe I didn’t understand you correctly?
Yes, there is a bug that sometimes after taming Lapine or some similar low-level opponent the game freezes. Unfortunately that one isn’t easy to fix, and would require reworking of the enemy generation system, nothing too huge, but will take some time which unfortunately isn’t available for this canceled project.