A stop() is a timeline level command, and a timeline can include several layers, meaning every layer on a timeline can be impacted by a stop() on one layer. I can't tell how you've designed your animation, so you'll need to explain that if my guess at a solution that follows isn't on target.
Create the one animation that you want to have stop as a movieclip unto itself. You can do this by copying the frames and pasting them into an empty movieclip symbol. Place a stop() at the end of the timeline inside that movieclip. Place that movieclip in the timeline where you copied the frames, in place of those frames.