Might be a pokeball bug. Try turning off the "catch players" option.
#died during my sleep??? what??? common/often reported bug or????
manic stream
latent cliff
If a player is in a pokeball at the end of a cycle that would definitely cause errors that could lead to this. unless the mod creator made something specifically to account for that
manic stream
Not yet 
severe warren
You both are physically in the shelter, right?
I know sometimes if someone’s in the pipe that goes to the shelter and then gets pushed back out into the next room it gets counted as a death
severe warren
Maybe test to see if it still occurs with every mod disabled?
Idk anything about better shelters/Pokeball mod so maybe having it on is the issue?
latent cliff
If you provide some exception logs of when the game failure happens we can look and see what might be causing it
manic stream
If you post your logs, it will help devs fix bugs in their mods. This is also helpful for other players, who will then not experience the same bug you did.
proven sleet
Might be because one person got glitched and ended up leaving the shelter while it was closing, happend to me before when I was controlling four scug with one controller