Maybe this is a rookie question, but can one upgrade on a Y/B fare using the PDA site?

This morning, a coworker had to book a last minute trip & called our TA to do it. We were in meetings all morning without proper internet access, but I checked him in using the PDA site since he didn't even know about that. He's a silver & it was a B fare, so I assumed that there would be an "Upgrade" button, as there is on the regular site. When I checked him in, there was an upgrade option, but when I hit it, it tried to charge me $35.94, which I'd assume is the difference between B & an F fare.

Any suggestions for the future when we don't have access to co.com? It didn't matter b/c the flight turned out to be 14/16 full in F and he got upgraded at the T-3 hr window.