I had the same problem however the lines didn't show any disconnection sign, passengers simply didn't come into the underground stations. On previous gameplay all lines were being fully used, stations used to be packed.

Deleting and placing new stations solved the problem for me but I have a feeling it will happen again next time I reload my city. By the way I haven't reloaded since I fixed them.

Would really appreciate some comment from author or somebody who knows what the problem could be. Thanks in advance.

There is a small problem with underground station as it no longer as Vanilla anymore with all the MOM default setting.
Also I did got a problem when no one use the Metro when the bus have 500 in the station. So I just relace the bus stop somewhere else and now they use the Metro. That is my case at least. Citizen may not regconize another transport option.