Revealing mistake: When Chucky's disembodied head tries to bite Andy in the beginning, watch closely. When the plaque he's mounted too leans forward suddenly as Chucky snaps at Andy, you can see a rod underneath of it, which was used to make it move and lean forward by the puppeteers.
Continuity mistake: When Andy is grappling with the "buzz-cut" Chucky and trying to rip his clothes off, at one point the camera cuts from a medium shot to a closeup as he rips Chucky's overalls down. In the medium shot, Chucky's left arm is reaching for Andy's wrist, but isn't holding it. But in the closeup, suddenly Chucky is grasping Andy's wrist.
Continuity mistake: Dr. Foley burns and melts the Chucky doll on his right hand with a lighter but when it cuts to a wide shot, Chucky's hand is completely fine.
Visible crew/equipment: When the patient throws Chucky into the hole outside, when he rises up, you can see someone's hand give her the doll.
Continuity mistake: When Carlos is killed by the three Chuckies with different weapons simultaneously, the editing gives away that three different prosthetic chest-pieces were used to accomplish the effect - one for each weapon. The blood and wounds on his chest and stomach are inconsistent from shot to shot as we see the different weapons slashing and stabbing him. His body also wriggles about a bit differently from shot to shot.
Answer: It's been years since the injury. Maybe she transferred her soul to another doll? Maybe she repaired her head? Maybe she copied her soul into another pristine doll as she can now inhabit multiple hosts at once? Take your pick, as it's a relatively insignificant matter.