Hi apple85
My feeling is losing shoes in nursery is kind of one of those things and [SPOILER ALERT] it won't stop there - both DDs lot a string of cardigans, fleeces, tights, socks, etc.... in KS1 and have gradually improved since starting KS2. Now Y4 & Y6 - we're down to 1 or 2 items a year.
I know that whilst in nursery my children did occasionally come home with other children's shoes/ toys/ clothes - but we always immediately returned them (washed if clothes) to the nursery the next day.
So my feeling is the test isn't that this happened but how they handle it afterwards. You obviously delivered your child with shoes on - so the question is what has happened and if the school will take responsibility.
Personally the likelihood may be that they were left in the toilets when she went to the loo (if she's independent) or was changed (if she's still in nappies).
I'm sure they'll turn up - but in the scheme of things - is she healthy, happy and generally well looked after? If so, genuinely, losing some shoes along the way, although I get it's annoying, is really small beer.
Finally I know that at our nursery the best time to talk to staff was in the morning, when they were fresh & raring to go. By evening they were usually exhausted. A day outnumbered by active toddles is hard work.
HTH