More importantly, they used the overcrowding excuse as a means to raise $800mm+ from New York taxpayers. If this capital wasn't necessary given the problems they cited were non-existent, this amounts to fraud.
1. Outdated signaling system cannot handle current load at high safety threshold
2. Network could not upgrade signaling system due to lack of money
3. Network responses by slowing down critical paths and putting in more locks
4. System capacity drops
So yeah, you still need the money to fix slow things.
Yes, the signals system needs to be upgraded if they want to increase the number of trains (and their speed) on the lines, but even without the signals system upgrades, they can still run the current loads at acceptably-high levels of safety.
Put another way, they are slowing the trains down and increasing delays while not actually increasing the capacity of the system.
Overcrowding is NOT a misc category, it is a specific situation with a specific definition (the exact definition is something they use should be published so we can decide if we agree with it), with specific training on how to tell if this is really overcrowding as opposed to a failure to get a normal crowd through in time since the solution to the two problems is different.
Other/misc is an import category to have - every system of collecting data needs to have a none of the above because there is always something you didn't think of. What is normally missing is that when other is used there needs to be a text explanation of what happened, and then an investigation to see what should be done. You collect data for things like "medical emergency" because from the category alone everybody understands that the delay is beyond control. When something is misc that means you didn't expect it and need to redesign your procedures so it never happens again. Thus the misc category should be something all operators hate to use: they get sucked into meetings on how do we ensure that it doesn't happen again.
In either case, probably time to clean house and get rid of the "better safe than sorry" crowd.