They used to hurt my foot too. I started paying more attention to the angle of my foot and that helped. When I first started doing lunges, I think my foot was more at about a 45 degree angle and that really hurt. So now, when I step my back foot on my toes, I make an effort to have the rest of my foot (the arch and heel part of my foot) as close to a 90 degree angle as possible. When I finally figured this out, it was a big relief to my tootsies. That also helped me realize I was wasn't using the front leg enough.
Hope that helped more than confused!
Best,
Liz