Right now in the squad builder, I can select extended game mode, create a new rebel team, add Luke Skywalker in an X-wing, and select the "predictive shot" force upgrade for him.

However looking at this site https://xwing-miniatures-second-edition.fandom.com/wiki/Predictive_Shot it seems to me that this upgrade card should not be legal for the rebel alliance.

Am I misunderstanding something, or is something wrong somewhere? Aren't upgrades supposed to be faction-specific now?

The same is true for "brilliant evasion"

No, it's a legal upgrade.

While some upgrades ARE faction specific, those Force abilities are available to use for any pilot with the Force upgrade slot. However, currently, those upgrades aren't available in any Rebel expansion yet. FFG has said that every faction would have a way to get every non-faction specific upgrade, they never said they would be available at the same time.

Alright, thank you