I'm currently setting up the armature for a character for my college project. However, I don't quite understand why the foot does this. If I set the leg's rotation to 90 degrees, it corrects it, but is there something else I could fix instead? I know that it's the leg's pole that's affecting it, but I don't know why. From what I can gather, everything is lined up correctly. I haven't had to set the rotation for the other bones with IK, either.
EDIT: Even when applying weight paints, the geometry for the toe/foot ends up being slightly angled. It happens if I set the rotation to 0, 90 or 180 degrees.