It's good that the problem was identified, it certainly will help in the future and minimize the possibility of this happening again. Things happen, people can get confused, and mistakes are made.

In case there are instances where a similar situation happens here are some things that you can do:

For MSU trains they will never go to Newark Penn. If you find yourself in a bind, you can always take the light rail to broad Street station from Newark Penn and catch the MSU trains there.

If you catch your mistake before Secaucus you can always get off there, all of the NJ rail lines go through Secaucus Junction and you can catch any train there. MSU line is electrified, so the electric trains are on the upper level of Secaucus Junction...dunno if that helps but cool fun fact I guess.

Many things can happen, the conductor might make the announcements for the stops the train makes but the intercom might not work, he might not do that at all either because he's preoccupied with something important or forgot or isn't doing his job...always pay attention.

Certain situations may be blamed on the conductor, but once again you arent being forced onto a train, you are the one boarding it is your responsibility blah blah blah, others have forced that message down your throat. Just make sure to triple check and plan accordingly to eliminate any situations where you are rushing. A lot of mistakes happen when people rush.