If we assume it's ada in the final mr. x fight, which it probably is, then ada must have escaped through some vent shafts.
Firstly, they were on the ground floor, the train-station was actually above ground. You don't see a lot of the station but i used to inagine there being some sort of link to the chemical plant/ factory. We know in REUC she escaped through the sewers outside the hotel, but i think she might of escaped back via the marshalling yard. I really think they ****ed up the realism with the ending scenes. Well, we know she escaped at least.