I thought it was pretty clear in the OP. 208/120 back fed transformer supplied with L1,L2, and L3 of a 208/120 system. XO happened to be bonded. Even though a neutral was not run the equipment grounding conductor and every other conductive path connected to it carried neutral current.
Simple solution is that the XO needed to be un-bonded and left to float.
Many people have posted this scenario in the past - most of them usually destroyed the transformer. They always end up being told to never connect anything to XO, as undesired current will flow if you do use XO.