Thanks TK and JayKiwi.

For future reference the answer to 'how do I escalate / fix' appears to be 'post about it on flyertalk'. As one booking cleared this morning, and the other this afternoon.

Got a call back this afternoon from an agent I spoke with so can add some more context:
- The upgrades had been skipped by the robot for whatever reason (child / infant / call centre upgrade? who knows)
- The team leader spoke with another team (presumably the loyalty team?) who said they would have to process manually - which they did very promptly

The agent was very diligent which I appreciate, I suspect if she had not escalated it would have stayed pending until T-7 or beyond (even though there were 5x R class).

As you say, trusting the robot seems high risk in anything but the most straightforward situations.