its just a tremendous snowball of fucked. in the 70s there was a budget crisis, which forced the MTA to fund everything through debt. that led to deferred maintenance and upgrades, which caused accidents and delays. those accidents led to train speed limits, which worsened waits
there are alerts but the issue is that all the trains are delayed all the time. they already run slower than most other trains, using inaccurate and broken signals that further delay them, and since they all share the same tracks, a single delay cascades across the whole system