The PUC Chairman took issue with an RTD spokesman's comment about the regulatory process.
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.