That's kind of what i was thinking - I know birds pull up onions and we've got a badger that comes through that would probably go for most things (although he's ignored the onions to be fair - took down the sweetcorn last year). Also I reckon the rabbits might have a nibble. So I think it's hard to be sure what's got them - in which case you could spend a lot of time trying to catch mice when it might not be. Maybe you could put a little mini-fence around them? I saw one today in the garden centre that was fleece and designed to keep carrot fly off your carrots but it would work equally well for mice and onions (but not birds). Or at this stage you could just put fleece over the top and surround it with stones and hope they don't dig under....
H