Unsure how this works but it seems to involve missing ID's of origins. The issue is that the player some times when they load in and the ID of the origin is missing, they get to pick the origin like normal, but for some reason, I had a few cases where the powers still remained of the origin that is now missing from the datapack, they picked all the missing layers fine, and have the powers of selected origins, but also have the previous powers of the now "missing" origin. Also at times I had issues where it just wouldn't allow to load in a single-player world and displayed "invalid player data" error message and unsure how I fixed it a couple of times.
It would also seem like I'm unable to get the "replace" field in origin_layers to replace default origins with custom ones, they just act as if "replace" was set to false unless I fiddle around somehow (needs more testing and only shows up to worlds that transition from 1.16.5 to 1.17.1)

Upon more testing, I managed to fix the "invalid player data" by removing all the players powers, and setting all layers back to "origins:empty"