The behaviour of APP should be that if multiple master flats are loaded and selected the first one should be used internally.
I think it would be better to warn instead of make assumptions or you should make it really intelligent: E.g. by determining the best fitting master based on the content the header of the subs versus the header of the selected master files (e.g. use the correct master file (Green) for the green labeled subs or the correct master DARK (60 sec @ -20C in my case for the 60 sec L subs at -25C).
BTW you might want to check if this occurs as well for multiple Master BIAS and Master dark files being selected unintentionally…