I would say, yes, it would have been nice for the GA to give you an updated paper BP upon boarding, and historically, this is typically what would have been done. This agent just may have gotten complacent to this particular procedure due to the prevalence of mobile BP's, especially among those FF's eligible for upgrades. I'm not saying the GA did the right thing by not giving you an updated paper BP, I'm just saying it was likely an error and nothing more.

Much of this thread seems to be around what's been commonly referred to as "shenanigans" on FT, when it comes to your upgrade and the pilot. This would have been a commuting (or otherwise non-rev) pilot, as opposed to a dead-heading pilot (if he were dead-heading he would have been automatically been prioritized ahead of you for the upgrade). While I suppose it's possible the GA was attempting these shenanigans, it would be quite bold and risky on the GA's part.

I'm a decades-long elite member, due to extensive work travel, but I am now also eligible for non-rev travel (for personal) as the parent of an employee. Through this, I have learned that there is a formal process for employees to report what FT'ers refer to as shenanigans. The other non-rev employees on the flight would have been watching the priority list like hawks, and they would have been able to tell if the pilot was cleared into first ahead of a revenue upgrade, and many of them wouldn't hesitate to report it through the company's official process. When these complaints are founded, disciplinary action is taken on the offending gate agent, and as such, these instances have become quite rare.

YMMV