I wonder if this happens accidentally or because of something. I ask about this because one day I had to change time on my phone (back in time), and then I opened TDS without remembering about it. Everything was very strange, I regret not taking screenshots. All the time meters were sticking out, the amount of time left was astonishing... So I quickly returned to my settings, changed time back, and everything changed back, too, but almost immediately one of my favourite bitizens got blown out.
It is the in-game penalty for changing the time.
Obviously, in a time based game, turning forward the clock would be an easy way to cheat. The developers have created a fairly minor penalty (compared to other games) to discourage this cheat.
There is no way to signal the game that the time reset was innocent. So, you were subjected to the penalty.
Just like in Tiny Tower, messing with the clock can randomly kill one of your Bitizens. In Tiny Tower it's a "time travel accident", the same thing happens in Tiny Death Star but it's a more thematically appropriate airlock accident. I'm not sure exactly how it detects messing with the clock, but the simplest way to avoid it is to simply not play with the clock.
I think the game detects when you mess with the clock if you make a mistake with changing the time. If you're at 11:00pm 7/25 and you tick the time ahead to 11:00am 7/25, you went backwards...it happened to me once because of that. I couldn't say if it happens every time or if that's the reason that it detects.