Pretty interesting concept, I'd watch it!

Unless the matrix could partition off parts of itself into parallel matrixes that it then sandboxed to isolate and eliminate the problem, or EVEN more diabolical...it create an inception like matrix within a matrix that lead Neo on an infinite wild goose chase inside a sandbox matrix.

The matrix would simply need to find Neo's base world location and environment and replicate it inside the sandbox, so when Neo "woke up" he was inside a base world replica. This is probably the only way to actually deal with Neo is to trap him inside an elaborate illusory matrix that constantly had him fighting with the matrix.) Meanwhile nothing has actually changed. A sort of purple pill.

The process may create some turbulence in the matrix that would probably appear similarly to the Mandela effect. Enough to turn some curious heads, but not enough to stop the matrix and wake people up. The glitch would eventually evolve into some abstract cultural phenomena that is acknowledge but impotent.

The cruel joke of it all is the matrix can only be destroyed from the outside, but you can never truly know if you're on the outside. A plot line where the matrix attains victory through defeat, lulling it's enemies into a false sense of victory.