This is not all that uncommon. I had a spoiled horse in to retrain several years ago. I used a soft leg to ask her to move and she laid her ears back and switched her tail. I was wearing spurs so I pressed a spur into her side and she cow-kicked my foot so hard and hung her toe on my spur that she nearly broke my foot. She never did it again! She found out that was not a good idea.
Anything you accept (like her kicking at your foot) is exactly what you are teaching her to do. It is just as sure as if that was your object in the first place. If you do not interrupt unacceptable behavior and scold or punish a horse in some way for the behavior, it will happen again but probably with more force and more serious consequences.
Just like a horse should be reprimanded for kicking at a person that is tightening a girth or brushing its belly, it should be reprimanded for any aggressive action while a rider is mounted. You should set firm but fair boundaries and and be 100% consistent in how you enforce them. Not only does that make the horse a 'better trained horse' but it keeps one happy and it keeps its riders and handlers safer.