A: I'd bet on either chipmunks or birds. I've had that happen, too.
Something is investigating as opposed to zeroing in on your young tomatoes for a meal. Otherwise, they'd likely all have been eaten to nubs.
To head off this problem, I set my transplants on a table in the middle of my patio. Rodents either don't find them there or are too nervous about venturing out into the open.
If it's birds nipping a stem or two, drape a little netting over them.