Honestly, I don't think it's worth complaining. I'm not aware of the specific problem of not being able to check in for mixed UA/US itineraries where the UA segments are waitlisted for an upgrade, but it sounds like their online checkin system just can't handle these sorts of itineraries.

You were able to check in online as you wished and you can always try to re-apply the CR1 after you print your boarding pass and see if it clears at the gate. Short of overhauling their entire IT systems while you wait on hold (which US could certainly stand to do), I'm not sure there's much else they could do that would allow you to check in online.

I don't think it's worth further aggrivation by complaining. I'd say pick your battles.