Unleash the power of 3D
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Hm. First i did a skinning to see the problem that you mention. No problem to see. Besides the fact that the bones points in wrong directions here and there.

So from scratch. In Edit Mode i selected the leg bones and did a recalculate bone roll Y positive, followed by a recalculate roll Z positive at the two toe bones. Then i skinned the rig. And i have again no problems at all. No deformations in rest pose. And also no trouble with posing. So we run into what i have feared. I cannot reproduce your problem.

What is indeed a bit difficult here is that the mesh is not symmetrical. So you might want to fine adjust the bone roll manually for the trouble bones, bone by bone. Best before you skin the mesh.

Hint, tick X Ray to see the bones in font of the mesh.

Hint, you can select more than one bone at once to do the recalculate bone roll.

Hope that helps a bit.