"The negative estimates in the final period arguably suggest different behaviour and/or exposure patterns in the vaccinated and unvaccinated cohorts causing underestimation of the VE. This was likely the result of Omicron spreading rapidly initially through single (super-spreading) events causing many infections among young, vaccinated individuals."

Yeah, I think it's more likely that this is the explanation. At least I'd need to be persuaded that the more unlikely explanation is the correct one.