My guess is that you're right; Lockpicking and Repair got replaced so Simians with the the Less Educated trait couldn't take them, though I'm surprised I did that after I'd done the creature write-ups.
Turns out you're right that the error pops up on immediately loading the portfolio; what id doesn't do, for whatever reason, is show an error on the skill tab (i.e. turn the tab red); that doesn't happen until I've modified the Agility.
So at this point, ignore my second bug report there, nothing to see here, move along...
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