Boston, New York, and Philadelphia have comprehensive commuter rail systems. And nearly all Amtrak routes in these areas share routes with the commuter systems, in and out of these cities.
New London CT
Amtrak's Montrealer briefly diverged here from the Northeast Corridor main line.
Amtrak's Vermonter diverges here from the Boston & Albany main line.
An interruption of service east to Boston, and the removal of a segment of track considered unneeded at the time, necessitated some creative detouring with a backup move for a few years.
At one time, two different Amtrak trains operated into Montreal, operating into two different stations.
The introduction of the Capitol Limited involving two different railroads, required construction of a new connecting track east of the station.
New Castle PA
The switch of the Broadway Limited to the Baltimore & Ohio route west of Pittsburgh, resulted in a new connecting track from the former Pennsylvania Railroad.