I have "Deformation" bones with Copy Transform of "Target" bones, so Deform bones deform mesh, and on target bones we put constraints etc. Everything was ok, and after Parenting bones to mesh with automatic weights and some additional weight painting I got this. When I move Control bone or IK - Deform and Target bones do not follow each other as seen on first picture. On the second picture they are overlapping on neutral pose, and would like them to stay overlapped as I move IK or Control. They are all Rolled on same axis, every constraint is put to Local Space > Local space. All transforms are applied.
If you have two bones with local->local copy transforms, and those two bones do not have the same parents, then they will not necessarily have the same world space transform. The local space transform of one will be interpreted in the local space of the other. Each of their local spaces will change as each of their parents transform.
If you want two bones to match each other in world space, then use world->world for a copy transforms constraint.