The two lines, which opened in 2016, have had significant technical issues with crossing arms that come down too early and stay down too late.
State regulators have denied a request that could have eventually led to the opening of the long-delayed G Line commuter train.
The emails show disagreement between the two agencies over basic facts and how to communicate them to the public.
A federal waiver that's allowed the trains to keep rolling while work continues expires this week. But officials say they anticipate getting another.