How can there be a non-zero voltage difference between Phase A on the left and Phase A on the right when they come from the same power source?
I don't see any "phase A" I see lots or a's b's and c's. 

However, I am guessing you mean at the panels. 

Since in your diagram, they appear to be isolated what you are reading may be a meter effect. 

However it is far more likely there is a common neutral / ground connected in there somewhere you are not showing us, in which case the transformers may not be connected the same way.