Do you work with 3DS max ?
If yes, you can use reset Xform tool to “re-orthogonalize” your bone.
De connect it from his parent before.
But be aware that the problem will propage to the children of the bone… So, you’ll have to do this with all the hierarchy Under your bone.
Before to do that, I suggest you to check if your animation is broken because it may be perfectly imported.
Non orthogonal axes are just a warning and may not causes problems 