Few fans seem to care that TNG's Relics threw a huge spanner in the works of Trek continuity. They all recognise that it did, but just make excuses to cover up for one of the series' best ever episodes.
It's a continuity issue but one that has been explained by Scotty being momentarily disorientated due to being stuck inside the transporter system for all those years.
In the book version of Generations, Guinan tells Chekov that Kirk is still alive in the Nexus, so that would explain why Scotty believes Kirk may still be around. Of course the novel itself isn't canon, so whilst the conversation between Guinan and Chekov never officially happened, it's not unreasonable to assume that it did.
Either way, its a fun episode.