I am posting ideas about why characters might not be rezzed as part of the game… .
if other DNA is present when you approach a Save point… (example: cannibal, Blood on clothes, etc…) then the DATA file will become mixed and would create a mixed person… multiple personalitys and different body parts. system could put out a alert to the person informing them about the error and allow them to select an option to not rez as a damaged clone.
The Teleports might read that there is already you in a different area and therefor will not rez what it considers a copy.
Jack could have turned off the teleports for a person to prevent them from escaping from him… like angel or roland. (could be a story about angel trying to escape from her father and almost succeeding)