I, like many, LOVED Final Fantasy VII on it's release and I've played through it a couple times. It wasn't until a recent playthrough of the original demo disc that I realized that the "flower girl" is on the top level of Midgar! I never noticed this because it's Midgar at night and it still has that same dark and dingy feel as the lower level.
Later when Aeris finds Cloud in the church, we learn that the Turks had been pursuing her for practically her entire life. This matters because we learn from Jess that if you are going to the top level of Midgar, the train scans the ID badges of all individuals at certain check-points. If someone is without an ID badge, or if they are on a hazardous persons list, the sirens will go off and Midgar police will apprehend the criminal.
Aeris is not a criminal but she couldn't have an ID badge because, if she did, she could easily be identified as the "ancient" that she is? Reno and the other Turks could then easily apprehend her.
Of course Barret, Cloud and the rest of Avalanche crew had fake IDs which worked well enough at least twice on both the trip up to the top level of Midgar to blow up the first reactor, as well as on the trip home to the lower level of Midgar. However, I seem to recall that these IDs were either expensive or hard to come by, so I doubt Aeris could have had a fake ID.
So... How did she get to the top level of Midgar?
If this is addressed in Final Fantasy VII Remake, I am willing to consider that a better and proper answer, applicable to the original source material.