I think one of the girls had a red gem but when they all did one super attack it was a giant super gem. There were two villains, one boy and one girl.
I watched it in like 2018. They had hair color and stuff based off their gems and could turn back into normal girls after the fight. I watched it on Netflix and it is not land of the lustrous
Based on the few details that you provide, I think you may be talking about LoliRocks. Which actually is not an anime.
Yet the details matches. Three girls (with more added later) using some sort of magic gem to transform, hair color changing during the transformation.
and two brother and sister villains, older than the three protagonists.
If this is the case you are pretty lucky, since there is an official Youtube channel that is posting all the episodes right now, available for streaming.
Reposting since it was a technically correct answer until the querent specifically said it was not this one, and it may help people in the future:
Land of the Lustrous, also known as Houseki no Kuni is mostly a match for the details provided.
In the mysterious future, crystalline organisms called Gems inhabit a world that has been destroyed by six meteors. Each Gem is assigned a role in order to fight against the Lunarians, a species who attacks them in order to shatter their bodies and use them as decorations.
Phosphophyllite, also known as Phos, is a young and fragile Gem who dreams of helping their friends in the war effort. Instead, they are told to compile an encyclopedia because of their delicate condition. After begrudgingly embarking on this task, Phos meets Cinnabar, an intelligent gem who has been relegated to patrolling the isolated island at night because of the corrosive poison their body creates. After seeing how unhappy Cinnabar is, Phos decides to find a role that both of the rejected Gems can enjoy. Houseki no Kuni follows Phos' efforts to be useful and protect their fellow Gems.
