You should complain if, for nothing else, to make them aware that their magic automatic upgrade mechanism that's supposed to remove just about all human intervention, is being usurped by employees. For #1, she absolutely knew there were others above the one she upgraded and she would have known if you boarded or not at the time time she manually processed the upgrade. The days when people can make nice nice with the agent and hope they get their upgrade are gone now that the transparency is there for all to see.

For the other one, it's even worse if you were on a confirmed J ticket. That would put you above anyone on the standby list who was not also rebooked for IRROPS reasons except deadheading pilots. They still trump all.