According to James Gunn, the writer/director of Guardians of the Galaxy Vol. 2, has provided an explanation for this in a Facebook Live session with fans:
“I actually read the Marvel fan sites and the Marvel message boards out there and a lot of times people have ideas that are somewhat off-base or silly or whatever,” said Gunn. “But one thing I found very funny and interesting is the fact that people thought Stan Lee is a Watcher… and that all of these cameos that he’s doing are part of him being a Watcher. So I thought that was one of the greatest things the fans came up with.”
“So, Stan Lee, as a guy who is either a Watcher – or probably a guy who is working for the Watchers – was something that I thought was fun for the MCU.
“And yes, I know I made a mistake. People have written and asked me, and I'll own up to my mistake because Guardians of the Galaxy Vol. 2 theoretically happens in 2014 which is before [Captain America Civil War]. And Stan Lee in the movie says, ‘That time I was the Fed Ex guy,’ which is what he is in Civil War. I screwed up; I wasn't thinking. That’s all that is.”
“But I'm going to say that – probably – Stan Lee used the guise of a Fed Ex guy more than one time,” laughed Gunn. “So it’s a mistake, but it can easily be explained away!”