I don't know what kind of setting you have your seedling flats located in....roly poly/pill bugs are one possibility in a damp setting, a mouse is certainly another.

Highly doubtful of a mouse, my cats have proven they are very good mousers. there is a door to a crawlspace right there though so I could duct tape it off and see if that helps.
I did see a centipede down there the other day when I was moving trays around a little-could that be a potential culprit?
It is my laundry room in the basement, I was worried my cats would be the ones wreaking havoc but they have ignored it so far.

Any slime trails? Slugs or snails can get indoors and cause mayhem if they find something green and tasty. Check under the pots and trays and underneath between the cells if they are in modular trays.

I agree with flora, you almost certainly have slugs, hiding during the day and eating at night. Put out slug bait before giving them any more plants to eat. Al

"I agree with flora, you almost certainly have slugs, hiding during the day and eating at night. Put out slug bait before giving them any more plants to eat. Al"

...just make sure it's pet-safe slug bait(Sluggo for example)since you have kitties...

I agree with the other replies about the slugs.

However, it could also be a cat. Can you close a door so that your cats can't enter that room? If your cats are anything like some of the ones I've owned, they get into a lot more mischief at night sometimes. I wouldn't put it past my current cat to eat my plants at night. I had a new door put on to keep him out. I love him but I don't trust him, LOL!