This app was mentioned in 1 comment, with an average of 1.00 upvote
From what I've noticed, countdown data seems to be relatively accurate based on a train's location, notwithstanding other factors. Think of this like how a 15 minute car ride might take you an hour with bad traffic. If the train were able to proceed from station A to station B, it would take exactly x minutes. However, if for some reason the train is delayed (someone holds a door open, train is extra crowded so it stays at the station longer, etc.) the predictions won't be accurate.
I'm sure that disabled trains only compound these inaccuracies greatly. Without knowing how the prediction software works, it's really impossible to guess exactly how a disabled train mucks up the system. Prediction software is very hard to do as it is. How do you know when the next train is coming? Is it based on distance? Is it based on a time average? Do you add time to accumulate for the extra rush hour crowds? Do you ever bump the time up? How reliable is the hardware? At what point do you take a disabled train off of the prediction board? Ad infinitum.
Personally, I recommend using an app or website that shows you where the trains are, not how long until they arrive. My app, MBTA GPS not only shows predictions, but also shows you where on a map the trains are. Sometimes I find this more helpful than the predictions; if a train hasn't move in 5 minutes, something is probably wrong with the train.
It would be interesting to have one of the MBTA software devs on here to answer questions about the prediction software and how it works.
Edit: To summarize my ramblings: I guess my advice for you would be to take the prediction information with a grain of salt. Just know that, for a variety of factors, accurate predictions are very hard to make.