This wasn't the only inconsistency in the finale (or Season 6), but imo I think it was definitely one of the biggest.
It was the writers trying to fool the larger audience into thinking that the entire 6 seasons mattered, when they didn't. Really, only seasons 5 and 6 mattered, what with the way they junked most all of the early plot lines in favor of Jacob. So, when the finale came, they picked and choosed which of the old characters and plot lines they would resolve, and which ones they'd leave on the cutting room floor. As a consequence, they were heavy-handed with pretty much everything they revealed, including the delivering of the "Adam and Eve" explanation, complete with the clip from the 1st season. Shannon and Boone reappearing was just another stab at trying to make viewers think that the writers knew what they were doing all along, even though we know that they didn't. Why not bring back Paulo and Nikki while they're at it?
The actor who played Mr Eko was apparently offered a big sum to make an appearance in the finale. According to the story out there right now, he asked for 5 times the amount from the producers and was turned down. So, what if he had accepted their initial offer? My guess is that he would've shown up as a quick-fix cameo, nothing more.