I've been instructing some new students and my CFI has been telling them to put their feet firmly on the pedals
I'm guessing that there has been a misunderstanding along the way. "Firmly on the pedals" doesn't necessarily mean "off the floor". At your experience level, I understand your apprehension about confronting your instructor, but they are your students and you have every right to inform them that it is ok to operate the pedals in a manner that feels most comfortable to them. Good luck.