riding the rollers does give tyres a hard time; the smaller the roller diameter is, and the lower the tyre pressure, the more the tyre flexes. There is quite a bit more rolling resistance on the rollers with any given tyre/pressure because the tyre is working harder than normal.
So if you are just warming up on rollers it is no big deal but if you are doing longer roller rides then I would suggest that you use some cheap 'sacrificial' tyres, not good/lightweight ones.
Not sure why the rear tyre should be suffering more on one side than the other, but is it possible that traces of chain lube end up on the tyre and this causes that side of the tyre to degrade a little more quickly..?
cheers