Yeah, as the title says: In Resident Evil: Extinction, Alice has been cloned several times by Dr. Isaacs. All those clones come out this kind of bubbles. In Resident Evil: Apocalypse, I thought Alice has been healed. Now I consider that she could be just a clone, too.
Has this yet been clarified?
According to the last movie, RE: The Final Chapter, Alice was a clone all the way along, starting with the original 2002 film. She was cloned after Alicia Marcus to serve as a secret operative / head of security for Umbrella, at a time when the Corp. already had succeeded with cloning technologies. This is also the reason why Alice does not have any memories of her childhood or parents; she only remembers the few events preceding the outbreak, e.g. her arranged marriage with Spence, her secret meeting with Lisa Addison, and the night before the T-virus was stolen from the Hive. There was no "original" Alice to begin with, as other answers suggest.
From this similar question on Sci Fi
The Alice who escapes at the end of Resident Evil: Apocalypse isn't a clone.
We know from the conversation in the sequel ("Resident Evil: Extinction") that the cloning programme didn't begin until after the end of "Resident Evil: Apocalypse" when Umbrella were unable to recover the original Alice.
Dr Isaacs : "Without the original Project Alice, progress has been difficult. I've been forced to replicate her using cloned genetic models"
On top of that, the screenplay explicitly refers to the Alice who escaped as being the original.
Resident Evil Apocalypse takes place within days to a month of the events at the Hive, in Resident Evil. Resident Evil Extinction takes place five years later. Even though Umbrella has cloning technology, it is not immediate. It takes time for the clones to be grown.
They also didn't know how much Alice was affected by the T-Virus yet. And had no reason to clone her until after the Raccoon City incident.
