Why does geometry deform in unexpected ways when using IK? 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.
This is a common occurrence when I set-up IK, I often set the pole angle to 90 degrees (sometimes 180 degrees) to fix the direction the knee points. I suspect it has to do with the orientation of the joints that are pointing to the pole in relation to the orientation of the pole itself.

However, because you can simply apply a correction to the constraint, I don't see much need to think over it further than that. There shouldn't be any problems with animation or posing due to requiring an offset to the pole angle in the constraint. So no need to worry about it ^_^

Edit: I just saw your edit. You should check that your skeleton is symmetrical on both sides. I've had angle issues like this before when the pole OR the leg joints were off by even a fraction of a unit. You need to make sure that your extruded pole joint is directly in front of (ie: same x-location) your knee joint.