I was stopped once on phase 1 of the MFL reconstruction.
This guy literally thought I would be a terrorist because I was filming out the cab window. Others that looked meh'ed him and one or 2 even told him this is America and we all have rights.
At 52nd where it was the temp. last stop, he told one of the main workers on the platform, the guy did not mind me taking photos, but warned me that other workers might not be so lenient.
What was funny though is the motorman recognized me from previous railfan trips on the MFL and had no problems with my railfanning on that day either.
No cop or anybody in general told me not to take photos. ACTUALLY, They(a good amount of police, septa workers, and neighborhood people) told me TO TAKE PHOTOS.
All in all, don't let 1 jerk ruin it for you, I had fun being in a construction only zone(Millborune Station).
So that pretty much cleared my whole day of that little disaster.
Anyways, to get back on topic, just have fun and be sure to post your photos after the trip.