Why do they use the same tracks?
Obviously they weren’t supposed to. They were traveling through a freight yard so speed should have been at slow yard limit unless they were on a faster bypass track. So the cause is one of four reasons — the engineer was speeding and could not stop in time, he ran a red signal, a signal malfunctioned, or the dispatcher routed him to a track already occupied. We will know soon enough as the modern engines have data recorders.
The commuter trains and freight trains use the same tracks all the time around here. It's very profitable for the railroads. If they had to build separate tracks, we'd all drive because they'd never get built.
Amtrak and freight trains share tracks. Amtrak actually owns only a pittance of track, mostly in the northeast and some in various other areas (e.g., most of the track Amtrak uses in lower Michigan is owned by them).
The US is short rail tracks like you wouldn’t believe.