One of the big problems with the Lionel subway cars is sticking doors followed by the flashing car light.
So lets take a look, first these are constructed like a fine clock or watch (side note I repair clocks) and the door racks (what the door is attached too) have very fine screw shafts with slide shoes. When these are dry and the door opens it will over travel compressing the shoe, by design this is fine. But when it is dry the do not release when the doors try to close the motor sensor detects the jam and stops the motor. I give a lot of credit to Lionel with that feature built in. So now we have flashing lights. First remove all four screws and pull straight up on the shell, now looking into the shell you see two center motors (one for each side) control boards limit switches and light bulbs. It can look overwhelming at first, no worries take your time.
So lets tackle the motors/drive gear boxes. First only remove one at a time, remove the tape that holds the wires in place and unscrew the two Philips head screws.There are two spacer washers one on each side be careful not to loose them. Now pull the motor/gearbox straight up the dog bones on each side will come out of the sockets they sit in, place the dog bones on the side (note all of the dog bones are the same size). Turn the motor over and look into the gearbox. turn one of the shafts by hand slowly looking for any missing gear teeth. Should you see on order a new unit from Lionel and wait for the part to arrive. If the gear box is fine grease it up and reinstall it (remember the spacers) . Now move to the door closest to the motor you just serviced. At the bottom of the door is a plate the the doors slide in, remove this by pulling straight up. Then remove the two screws that hold that door in place. The other dog bone will pull out of the other door (they are all drive together.) Turn the shafts and grease the screw shafts and slide shoes, grease them and open the doors by turning the shafts, do this for the last door as well. When installing the doors line up the slots in the cup that dog bones go into, open all the doors you just serviced and then start to close them until the slots line up. Put one dog bone in and then line up with the next door screwing everything back together. Keep an eye on the limit switches as one of them will have to be compressed to get the door mechanism to seat properly. Only do one set of doors at a time and one motor/gearbox at a time.