I believe it is more of a repair joke. During times when you go into the repair screen the clock can start going to negative if you just wait there.
It rarely happens but I've encountered it a few times where my subs sudden slip into negative time.
Or it could be expedition timer joke as well but I never seen the timer go negative for that...yet.
Edit: nevermind. It seems the joke is about Ushio escorting Wakaba and getting lost, probably in an expedition, ending up just moving while sleeping. Based Ushio.
Updated
Ushio vs WakabaAnd then?Maybe we'll need at least three ships for patrol workWakaba is unconscious and Ushio fell asleep. Seems like they kept on cruising like that until someone found them.