There are a few things you can do…
First, try squatting with blocks under your heels (these can be plates, a 2X4, whatever). If this fixes the problem, then work on ankle flexability. You can slowly reduce the height of the block over time.
Also, try to take a wider stance. For many of us taller lifters (I don’t know if you are, but I am), we need a slightly wider stance in order to go deep without going up on the balls of our feet or falling backwards.
If that doesn’t help, try squating with your toes off the ground, raising them as high as you can, focusing all of your weight on the heel.
I have been doing some reading last night and a few sites did mention to try placing a 2x4 or some sort of elevation plate underneath my heels. I’ll have to try that out.
Also, I do happen to be on the tall side, 6 feet, but I don’t feel like that is tall enough to be causing the problem. In the mean time I’ll try working on my form. The weird part is with my own body weight I can stay on my heels, but as I add more weight the heels start creeping up.