So, my advice to her should be to ask the gate agent so that she can be added to the list?
I'm not hoping for too much -- this is EWR-SFO after all, but still, a benefit should be automatic / at least correctly done in form, "to avoid confusion" as United now says.
Why would the itinerary confirmation say "CPU requested" and yet it not happen on check-in? This is not very smooth...
The checkin agent ought to be able to add her to the list, but the GA can as well.
The hypothesis is that the CPU eligible notation simply means that the website logic examined the reservation and noted that it should be eligible for an upgrade. It doesn't actually examine the state of the upgrade waitlist or anything like that.
At any rate, I'd say she has a snowball's chance in hell of clearing EWR-SFO so I wouldn't put too much effort into fixing it.