I'm sorry, they complain about emissions from trains? The electric Amtrak trains? From within a tunnel? While they're surrounded by streets will all kinds of car traffic? Freight trains are routed the long way around the city btw.
Directly across from the elementary school Amtrak plans to build a ventilation facility to “provide protection for train passengers in the event of an emergency,” according to the Amtrak website. This structure will include emergency fans that “could extract smoke from the tunnel in the unlikely event of a fire.”
If something goes wrong, they vent the bad air coming out of that tunnel across the street from a black elementary school. Their planned management of hazardous emissions is what’s in question.
I don't know the specifics of this project, but not all Amtrak trains are electric, they also run diesel and dual mode (diesel/electric) trains (I'm pretty sure, but not certain that the northeast corridor is all electric)
There's also other things worth considering like emissions from construction or maintenance vehicles, some lines are used for freight and passenger rail, construction might stir up any crap that might be in the soil, I suspect there's some amount of metal dust created by the constant grinding of wheels on rails, plastics from brakes and such, leaks from any hydraulics onboard the train, refrigerant leaking from the air conditioning, etc.
In the grand scheme, even if they're running straight diesel trains, leaking fluids, asbestos brake pads, etc. it's probably all negligible in emissions compared to just living in Baltimore, maybe even offset if it leads to more people using Amtrak instead of driving but all of it is still worth considering.