Edit: Ignore the ramblings in here for now. Not fully confirmed, but infinite food storage (drop food into a C02 pit) does not play nice with a small amount of toilets and/or overlapping offset break schedules.
After a lot of testing, I have found why they do it. I thought it was some other issue but it's simply that bladder is a 1:1 cycle ratio, and due to RNG, they may or may not get interrupted when eating to use the bathroom. If you don't give them enough time to waste running back and forth and getting to 4kcal before bed, they will leave it on the floor to rot unless you have storage space and someone to clean it up the next day (losing freshness). They even seem to run off to the recreation area and never come back to clean up their mess.
Even with a 1:1 ratio of toilets per shift, the only way to reset this is to lock them in the bathroom at the start of the downtime... No that doesn't even work because they wait until 100%. Yeah, it's just RNG. Once they get derailed, they will stay derailed until RNG fixes it back. They will try to eat first, and will use the bathroom at the same time each cycle, so it will keep happening until they waste enough time one cycle being far away to have to use the bathroom first. Even then, I'm not sure it will correct itself and it will happen again anyways.
I would say give them more downtime but this is already with 5 slots of downtime and I haven't even went that far from the starting area. They just sit in the recreation room letting it rot.
Steps to Reproduce
Have a dupe start eating near 100% bladder. Have full food storage. Have lots of sterilized food on the ground. Have a recreation area.
This issue has not been confirmed by a developer yet.