Any trauma to the skin can cause pigment to be distributed unevenly when it heals. Probably, over time, it will even out, but sometimes not.
I got shot under the right armpit point blank with a paint pellet gun in 1983. The overpressure from the impact broke a lot of blood vessels which blew through my skin, leaving what looked like a perfectly round scrape. (It was as weird an injury as it sounds, and hurt like hell because the skin there is so thin and delicate. Looked exactly like road rash, but that's not what caused it. ) I have a round freckle there about the size of a quarter.
So, your freckles may fade, or not, but it's normal to have uneven pigment after something like this.