The first thing that's important for you to remember is that quite a bit of time passes between 3x07 and 3x09. It's unclear just how many days/weeks pass between 3x07 and 3x08 (it's definitely at least a few days, though, since Olive is on a senior retreat in 3x08), but Saanvi mentions in 3x09 that they've been testing on the driftwood from the Vatican for 33 days. They started those tests in 3x08, so a month passes between those two episodes.

That means that Angelina has been acting more and more like Olive for a whole month. She's been borrowing Olive's clothes since 3x08, getting closer with Grace, getting involved with Grace's family restaurant, and acting like Eden's big sister. Some of her phrasing also makes Olive feel like Angelina is trying to push Olive out of the family, instead of trying to create a space for herself. And now she's even dyeing her hair to look like Olive's.

What's important to remember here is that Olive has felt like an outsider to her own family before. At first, she and Grace were together in that:

But then Grace gets the Callings too while she's pregnant with Eden. And while Olive's biggest fear at this point is losing her family in 5,5 years, that doesn't mean she doesn't still feel like an outsider at times:

This feeling is something that helped push her to the Believers and that to this day hasn't fully been resolved. Which I think is a huge part of why Olive responded so poorly to what Angelina was doing. Angelina is a passenger and gets the Callings, just like half of Olive's family. She gets along with everyone and seems to be fitting in really well at this point, at least from Olive's POV. In fact, Cal has been waiting for her, so clearly the Callings want her with the Stones. I think it's completely understandable that Olive would feel insecure because of this and get more irritated with Angelina as time passes, until we finally get to her outburst where she tells Angelina that the Stones pity her.

I don't think Olive really meant that, though. Her face after Angelina runs off tells me that Olive immediately regretted saying that, even if she was still feeling uncomfortable about Angelina's behaviour:

Olive's only 18, and she's allowed to make mistakes. Teenagers mess up sometimes. Especially when they feel threatened and insecure.

Talking with Grace, however, makes Olive realise that she's not being fair to Angelina and that she's not seeing the situation from Angelina's perspective. So she goes to apologise to her and leaves her several voicemails. Olive's not unreasonable and is able to admit that she's made a mistake. But Angelina crosses a line when she tries to kiss Levi, whom she knows Olive has a crush on, and I think Olive's anger is absolutely justified here.

I think there's also an additional layer to Olive's changing feelings towards Angelina here that's less evident. As we now know, Angelina was being built up as an antagonist, who would eventually join up with Adrian and Eagan, kill Grace, and kidnap Eden. I don't think we're meant to see Angelina as an evil person, but she's certainly a very troubled and malleable person. When she put on Eden's clothes in 3x08, the score was pretty ominous. And after Cal promised her he'd keep her wearing Olive's dress a secret, he got the vulcano Calling again, followed by the one where we see him, Ben, Mick, and Angelina all scream together. It suggests that their lifeboat is in danger. After the season finale, we can interpret this as the Callings trying to warn Cal that Angelina poses a danger to their lifeboat (probably on top of the danger that Saanvi's research posed).

During Olive and Grace's talk about Angelina in 3x09, Grace says that Angelina looks at Olive and sees someone who has it all. Olive says it doesn't feel like that. At first glance, that could just be seen as Olive saying that she's having a hard time putting herself in Angelina's shoes and looking at this situation from a different perspective. But now, we have to wonder if Olive's feeling about Angelina may have been more than that. This show has been hinting about Cal and Olive's twin connection being special since season 1. It's possible that while Olive doesn't get Callings, she does instinctually feel more than the average human because of Cal and Flight 828. It could be something that's similar to Zeke's empathy powers. Whatever it is, Grace tells Olive that she was right about Angelina in 3x12.

So in conclusion, I think two things were going on here. Angelina's behaviour was playing into Olive's insecurities about her place in her own family, and Olive was acting based on a feeling that she can't quite explain but that ended up being right. That doesn't make her compassion for Angelina in 3x07 any less genuine. It just means that Olive's behaviour changed based on the way Angelina's behaviour changed.