I have noticed this on more than one occasion. I assumed there was some other event (possibly hidden) that extended the end of the project and the automation continued until that event.
I also have motorized faders on my surface but I think this happens even w/o a surface.
Like you, I just selected everything past the automation fade-out and deleted it. The first time it happened I spent a lot of time looking for the bogus event but now I do not bother, I just delete everything past the project's end.
I wish the Bakers would add a simple end of project marker that stops playback no matter what and also truncates any editing, bouncing, and so on to the end marker.
I will handle reverb tails, stuck MIDI notes or other complexities by simply moving the marker if need be.