If the timing of your days was correct, the opened cell could not of been a fully developed queen. Probably a bad queen cell that the bees were removing. You can lose a cell every now and then throughout the entire process and the bees will rip the cells back down.
I usually start taking mine out by on day 13. That way if bad weather or other situations come up, I still have an extra day to place cells in mating nucs. If I wait till day 14, then need to finish up the next day (Day 15), you run the rick of an early queen,...and of course dead queen cells.
Queen (larvae and pupil stage) should never be handles or move prior to day 12. Up to day eleven, the queen is still in contact with the royal jelly plug. If she loses contact she will starve or be damaged After day 11, she is no longer in contact and has everything she needs to finish developing. As long as she is not chilled (as MB stated), or bumped to hard (wings are the last to fully mature) she can be moved and placed in mating nucs. But the closer you get to day 14 the better your odds of not having something go wrong.