Did you make the alien nests harder by any chance? I got 3 golems on the very first nest, and just generally (seemingly) more enemies on each.
That aside, my submarine came to a complete halt after sustaining some extensive damage. Even though my batteries are full, the current speed bar in the maneuvering system is just shimmering at one block:
Is that intended? I feel like it has to trigger a loss, otherwise the player is just stuck in limbo :)