Unfortunately, thanks to a combination of poor design choices and poor upkeep, many of these speedometers have proven to be wildly unreliable. So, as train crews navigated the increasingly speed-controlled subway of the aughts, they not only had to build uncertainty around signal design, but equally about the accuracy of their on-train equipment.
In other words the problem is both inaccurate signals and inaccurate speedometers. The combination requiring operators to be much more careful, and making them lose faith in their data. Exacerbating this is that signal trips caused by faulty timers were still blamed on operators. Making them also lose faith in management. Presumably, this wasn't good for the relationships between management and unions, hence probably contributing to strikes.
In other words: the conductor might be operating the train at a perfectly reasonable speed according to their accurate instruments and the track signals, but the track signals are no longer calibrated for their trainset or the upgrades done to it over the years. This has made conductors excessively cautious, precipitating the recent slowdown crisis on the subway.