I'm trying to rig the wing of a bird (I'm following the piero training course of the CG Cookie) and I noticed that two bones are out of place. Since the author of the tutorial used a lot of constraints and became a mess for a newbie to understand,I would like to know if there is a method to know how to fix the bones that are misaligned when a lot of constraints have been used. thanks.
There is no automated function for fixing false constraints, because there is no way blender knowing whether this constraint is doing it's intended job right or wrong. You have to fix this manually.
The only automated feature, is "clear transform" (type it after pressing SPACE). but this only resets your animated translation, scale and rotation and will most likely don't fix your problem.
You actually have to manually click through every bone and disable and enable the constraints (by clicking on the eye icon of the constraint), to find the wrong constraint and fix it by hand.