It's a high-speed crossover that is pretty lengthy from start to finish, with no discernible speed dropoff ahead of the switch because of the 1500 ft. straightway it's on under Beacon St. The split happens between Maitland and Miner Sts. (little closer to Miner) >1700 ft. past the Kenmore platforms and <800 ft. from the C portal. The D does a little S-curve through what's now that surface parking lot to get on-alignment for the Fenway portal, but that curve doesn't start until crossing over through the open-cavern portion of tunnel. I don't know if there's a permanent yellow signal or not; outbound is the only place you'd ever notice it because inbound this switch is too close to the portals to get going fast enough. In general this is zippy tunnel because the C portal is straight and long while the D junction is "modern" 1958 construction on geometry.
Riders felt the car strike the tunnel wall, and the strike point is clearly visible on the center truck. Rear truck stayed railed on the crossover making it to a stop at the C-Inbound track's frogs. Center truck derailed. And the photo of the front truck sitting in the divider-wall portion of tunnel is too grainy for me to see if it's completely on the tracks, or just mostly. The problematic center section moved the most laterally, though it didn't have to be the one to come off the tracks to jackknife like that.
T rules out any mechanical fault with the track structure or junction switch, so we're down to: (A) car, (B) human error, (C) fluke as potential causes.