After a bit of looking around this is apparently answered in the novelisation for _Resident Evil: Extinction_. In short when Alice was captured at the Detroit facility Dr. Isaacs programmed her to obey his orders, as we've seen a few times in the films, and one of these is to kill Angie.

> Peering into the SUV’s backseat, he added, “And I see you brought a friend. Very considerate, as we were wondering what happened to Dr. Ashford’s unfortunate daughter.” He sighed. “Still, I’m afraid she’s not terribly useful. The form of the T-virus her late, lamented father infected her with bears very little resemblance to what’s floating about in the air now. It’s mutated far beyond her ability to be useful to us.” Isaacs straightened up and looked right at Alice. “So I’m afraid you’re going to have to kill her.”
>
> Without hesitating, Alice unholstered her weapon and aimed it right at Angie.
>
> <sub>_Resident Evil: Extinction_, Chapter 16</sub>

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> The bullet ripped through Angela Ashford’s head, splattering her brains all over the SUV’s rear window.
>
> In her mind, Alice screamed, Noooooooooooooooooooooooooo!
>
> <sub>_Resident Evil: Extinction_, Chapter 17</sub>