I would say there was something wrong with your WT plasmid, sequence, or quality.

How is your transfection efficiency?

is the Flag fused to something in your WT plasmid? if not only a short protein is make that run out of the gel. does it have a start codon? did somebody used the wt plasmid before? maybe the wt has a mutation that you corrected doing the mutant... did you sequenced the wt and mutant genes?