What's worse, CdeeZ, isn't the bearing staining, it's the surface shear failure in that same photo. Look on the gear teeth at 8 and 9 o'clock, you see those tiny pits on the involute face? That is the material failure. They will only get worse, and there's nothing you can do to fix them. Maybe it's just dirt, but to me, that's the textbook pitting of a surface shear failure.
I noticed the same issue. But without knowing the condition of the transmission before installation I didn't want to assume all of the damage was due to towing. If the damage is due to the current application, it seems like the transmission has survived long enough to suggest that it may be worth investing time to improve it's chances.