You're not being clear in your description. The issue is that the bonus afforded by a used mutagen does not take effect after loading a save. The only way to get it working is to remove it from the slot (move to inventory), and then place it back. This bug has been reported before, and someone from CDPR said they'll look into it, or something to that effect.
By the way, there is also a different bug with alchemy, where you can't craft a mutagen (game says "already have this item"). With that one you have to drop the existing mutagen(s), and then you can craft the new one.
I hope both of these bugs get fixed soon, they're pretty annoying.