Control points function similar to bonfires in Dark Souls. They are checkpoints where you health up, upgrade weapons forms, purchase abilities etc.
This is almost unmissable unless you purposely choose to not cleanse Control points during the story. There are 29 control points in total, and all are in obvious paths during main and side missions. Sometimes you can just claim a point as you find it, other times you have to take out a wave of enemies before being able to take it. They have a noticeable blue distortion swirl around them, and similar to collectibles a very obvious button prompt. As long as you take all control points during your main missions, you'll have this done before the main story is over.