The automatic system was fine for nearly 40 years. The upgrade process killed nine people and injured 80 and caused a safe system that ran reliably for nearly 40 years to run in "manual" mode for five years because of a maintenance error.
Several depositions from railroad workers who were tasked with upgrading Metro's nearly 40-year-old system mentioned a real problem. The signals were "bobbing." This happened because the older signal system was being replaced with a different vendor's technology in two phases with catastrophic results.
In phase one, the lineside signal cabinet equipment was replaced but the original track sensors were left. In other cases, it was reversed: the track sensors were replaced but the lineside signal cabinet equipment was original. In both cases the vendor was different and not totally compatible.
Naturally, as we would expect, the two different vendors' equipment was not interfacing perfectly. This caused signal "bobbing," where track occupancy would "bob" from red to green repeatedly. Trains would vanish from the system. Phantom trains would appear in the system.
This massive oversight reported in the depositions wasn't really taken seriously in the press nor by the accident investigation. From this point of view, the system failed due to incompatible equipment made to interface in order to save money and service disruptions. They didn't interface properly, and people died as a result. Nobody seems to care about what appears to be the real problem: incompatible vendors made to interface to save time and money.
But we now have faster trains with shorter headways that sometimes fail to stop at the correct spot in stations, so we have that going for us. At least the lineside cabinet equipment and track sensors are now from the same vendor, eliminating the problem that killed those people and put hundreds of thousands of others at risk for a couple of years until that deadly day in 2009.