There are at least three possibilities, with each having pro and con arguments. Ultimately, it is up to the viewer to decide which of these reasons is the "correct" one. In order of likelihood, they are:
1) The girl was Connie; his seeing Donna was a "cross-chatter" hallucination caused by too much Substance D.
After being rejected by Donna, Arctor picked up a "Substance D whore" named Connie and had sex with her (in exchange for a handful of D.) He wakes up several hours later, looks over, and sees Donna in bed with him, then shakes his head in shock, and the girl has returned to being Connie.
Later, in "Agent Fred Mode" he watches the scanner replay of the scene, and essentially the same thing happens: the girl starts off as Connie, turns to Donna briefly, then returns to Connie.
Just before that last incident, the two doctors who had done a Substance D Impairment Evaluation early in the film call him up, and ask if he's experiencing any Sub D symptoms. They specifically mention "cross-chatter" where you look at one object but perceive another.... such as looking at a card of a dog and seeing a sheep.
The sequence serves two purposes: (1) it shows that his brain is indeed suffering from cross-chatter from D abuse, and (2) his brain is splitting into competing Arctor vs Fred spheres, and it is clear that Fred does not realize that he is watching himself on the tape: he does not remember that the same thing had happened to him (as Arctor) only a few hours or so earlier.
2) The girl was Donna, and Arctor was having a "cross-chatter" episode that made him see a random girl (Connie). His seeing Donna briefly was a "moment of clarity."
There are a couple of problems with this being the answer. First, The girl is clearly shown taking some Sub D, and it is later established that Donna does not do any drugs. Second, the girl sleeps over, which would be very risky indeed if it was Donna, as Arctor could very well wake up later and start seeing clearly, thus realizing who he had really been with.
Of course, it could be counter-argued that if it was really Donna, she was just pretending to take the pills, and that her pre-sex dialogue with Arctor was skillful acting on her part: asking questions about who the people in the living room were, where the bathroom was, etc. Donna would have known these things, of course, but was pretending to not to as part of the role of being someone else.
In the book, it is mentioned that Arctor had met Connie a few weeks previously at a party and had been carrying her number around with him since then. This detail is omitted in the movie, and it is not explained how Arctor met Connie, so one must also factor in the difficulty of Donna managing to be in the "right place at the right time" for Arctor to have picked her up after leaving Donna's. It is unlikely that Connie is a "curb crawler", as a professional prostitute would almost certainly have left after the sex so she could get back to business and new clients. So if she was just some "party girl" then Donna has quite a task of getting to be where Arctor would pick her out and up.
3) The girl was Donna wearing some sort of futuristic disguise, such as a scramble suit set to one image (Connie).
While Bob's initial reaction suggests it the "cross-chatter", his analysis of the recording of that night show that what he saw in person, he saw on tape too... When he pulls the image, he turns a device on and off repeatedly that has something to do with the video feed... it subsequently turns the image from Connie to Donna and back again... This device seems to cut through Donna's disguise.
There are multiple problems with this reasoning. There is a specific animation style to people wearing a scramble suit, and this is manifestly missing in the sequences. Also, one has to wonder how to have sex through a scramble suit without Arctor noticing this. Of course, people can smoke, drink coffee, and pop pills while wearing a suit (a known goof, see above) but sex-through-a-suit requires much more suspension of disbelief. Also, the same problem of "Donna" spending the night exists: the longer she stays, the more likely that Arctor would discover he was with someone other than Connie. Finally, the exact function of the device that "sees through the suit" is not known, and can just as easily be explained as it all taking place inside Arctor/Fred's head... especially when he was able to see Donna without the use of the machine the night before.