During certain cutscenes, like flushing an item for the first time, the game some kind of creates a savestate before the cutscene and, after the cutscene, it kind of restores that savestate.

It's happened to me once that the game didn't create the savestate before the cutscene. So, after the cutscene, it restored a savestate from a previous run.

Right now, nobody knows why this happened. There is precedent, though: in Monkey Island 2, there's a c99 glitch that can be reprduced and seems to work in the exact same way. In that game, the file extension of the file containing the savestate is c99. According to mikeSpeedyAdventures, the file extension in Day of the Tentacle is c00.

In case somebody would like to look into it, here's a video showing the c00 glitch. At 4:37 in that video, the game restores the content that was autosaved at 1:36, during a different run.