never had this issue. I have messed up scenes before, but always due to operator error.
Sometimes I have applied settings to the wrong track, in error. But more often the mistake will be application of a setting to an input rather than the target track. This, for me, is more related to the selection of the "layer" on the 2400. >> Much easier to be looking at inputs instead of tracks. On the G and 1600 there is not a "layered" display so the mistake would need be more "deliberate".
But I'd check out the similarly numbered input.
Also, this can be another pitfall of using scenes within a Tempo Map. But if you are not "automating" via a Tempo Map, then not an issue. On the 2400 though, using Automix this is definitely an issue, as a scene gets called up every time you RTZ >> Play.
Sometimes scenes get saved to the wrong slot ???
Important scenes need be protected so you are prompted to be more measured in your procedures. Let us know if this persists. there was a another unusual system issue in a recent thread, where tracks seemed to mysteriously be malfunctioning.

Hopefully both mysteries will be somehow explained...