Depending on what type of laser is used for hair removal, it is definitely not uncommon for freckles to turn darker.
Most laser hair removal systems target the pigment that is within the hair shaft and because they target pigment, they can have the side effect of treating freckles or other darker skin lesions such as lentigines. Once the freckle turns darker, it typically essentially flakes away slightly one to two weeks after the treatment and is now a lighter color. There is typically less darkening with each successive laser hair removal treatment as the freckle itself is actually lighter in color. Should you end up getting sun exposure between treatments resulting in darkening of the freckle, this will once again be treated by the laser hair removal system and resulting darkening will again occur.
We therefore highly recommend patients that are undergoing laser hair removal treatments to wear sunblock so that this does not happen.