In the image below, just left of center, you will see a open cell with a pupa in its 'purple eye stage'. Since the other brood cells surrounding this are capped (developing into adult bees), this is a sign to the beekeeper that there is something wrong with it and the bees will soon discard the pupa.
Here is a close up of a pupae in purple eye phase.
(Image courtesy of http://www.caes.uga.edu/)
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