Sore feet from fly stomping?

my horse has been a bit sore lately. not lame, she just takes a few weird steps here and there, and its enough that i can notice theres something wrong. one of the instructors at my barn said that her hooves could just be sore from stomping too much because of flies. is this possible? if so how can i help her stop stomping? i have a fly sheet on her and i fly spray her every day.