According to the SF2 Playtest errata 3, Operatives should begin with expert Will Saves. This is correct in the compendium and the character builder when viewing/reading the class, but when selecting the class it only applies trained to will save to the characters.
Thanks for letting us know this isn’t working right. I’ll pass it along so that we can get it fixed!
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Based on a quick look here and there, it seems like most of the wave 3 updates from Paizo haven’t made it to the Starfinder 2 character sheet, with this one being just one example.