I've seen the same thing (or something akin to) happen a few times - and haven't been able to crack the code or solve the enigma?
I find it especially mysterious, when it happens among the multiflorals, e.g. my recent St.Swithin, where the first flower to open had a slight 'horn'/'dentation' on the labellum, which is completely absent in the other 3 flowers; or suddenly in one flower among the succesive flowers of a plant in section cochlopetalum, e.g. my P. victoria-mariae (that are flowering in the "cooler section" on my back stairs at home): after several perfectly formed flowers...suddenly a dentation on the lip...the next flowers again no sight of such a thing? I can't exactly remember, but maybe the dentation showed up a little while after the use of an insectiside to kill off a light invasion of mealy bugs?