Can the light used in optogenetics change the brain it is meant to control? · Grey Matter

Yes, through heat.

Can the light used in optogenetics change the brain it is meant to control?

Yes, through heat. Part of the light delivered through a fibre is absorbed by tissue, and modelling and measurements show that light powers within the range used in experiments can warm the tissue near the fibre tip by around a degree or more, which in some conditions is enough to change firing on its own, in neurons that carry no opsin at all. Careful experiments therefore keep light power and duty cycle low and run the same light in animals without the opsin, so that any effect of light alone can be subtracted from the effect of switching the cells.