I have a lot of experience with high-rep squats, and I’ve gotten foot pain during them. My suggestion would be to try changing the lifter’s shoes and/or his stance. If he’s using soft-soled shoes, he’s not doing himself any favors. However, I think the pain may just come with the territory. If you have a heavy weight on your back for 2 or more minutes, it’s going to cause some discomfort.
I still occasionally get foot pain during squats. I most recently had some pain in the arch of my right foot, so I just sucked it up and then took my shoes off after I finished the set to relieve it a little. Next workout, I didn’t have a problem.