This can happen in IK_Strech mode with some bones attached to the main skeleton. Those bone need to scale in 2 dimensions instead of 3. You can either manually try and add different constraints to limit scaling to 2 dimensions or just avoid IK_Strech if it becomes too complex.
You could try setting the default Copy Transform constraint to 0.0 on the affected deform bone.
Then add a Copy Location and Copy Rotation transform with the same parameters. This should fix most issues but the real fix is to come up with a constraint mechanism that only copies scale in the correct 2 dimensions.