I've repeated this with Virus against AI1. I cast Afla on the Virus, infected a random creature, played a Virus to the same slot, and cast improve on it. At first it was a GotP with some skill, but then it remutated into a Malignant Cell with 1 other cost Destroy. Didn't get to use ability, TStorm killed, and playing a Virus to the slot and improving didn't repeat the bug
My guess is that statuses are tied to slots, and the aflatoxin slot triggers the slot to be filled with a Malignant but the mutant status also remains
Random test: mutating something with alfatoxin counters does not trigger a malignant cell mutant
Another random test: Malignant Cells on field. Aflatoxin on Virus, followed by Virus sacrificing, then wait. Malignant Cells reproduce over the slot, and the malignant spawn effect occurs twice on that slot