this happens... even with great care this happens. not directly related to nucs but to package making.... I don't know how many time I have gone with folks to shake packages and much later when we were unloading (several hundred) packages (at this point without queens) and found a queen clinging to the outside of a package. a queen can still fly and it is not that unusual 'when' you do these sorts of things to have virgins flying and both can and will end up in almost any 'box' of bees with little problem.
ps... I have long used the doolittle method of nuc making and the same thing can happen there if the queen (which was suppose to be in the bottom box) ends up in the top box when you pull bees and brood for nucs. it is hard to figure out exactly how the queen got there but the evidence is clear she did. to reinforce a point 'when' we do these things matters and the potential of capturing a virgin or newly mated queen is also not insignificant.