In my experience the system does this when you're better off not using the pass as the base fare of the regular ticket is lower than the fixed base fare of the pass.
What is the route and the base fare (excluding surcharges) that you're looking at?
The base fare is $2245.48 and YQ is $29.52 with T + G bucket.
If I use the pass, the system only offers me T + T bucket, with a base fare of $2525.
(There is a different date with G + G available both ways on regular cash ticket, but as soon as I use the pass it bumps me into T + T).
Edit: Finally reached the companion pass department on 5th try, after asking a concierge to put in a callback request with a manager in that department.
Unfortunately, the agent couldn't price it in T + G with a companion pass either. She told me that she saw availability in G-bucket, but as soon as she grabs it and prices the itinerary, the system forces it into T-bucket. I guess I will just have to eat those $280 more expensive charge if I want to fly this ticket.