I suspect that project organizer plugin parses some files twice, when opening a project with "Index all project files" set o Yes or Auto.
The reason for this is that the plugin parses all files but then Geany itself parses all opened files (or maybe the other way around?). So if you have a project that has many of its files already opened, it might make the opening of project needlessly slower. I believe that the plugin might safely skip files that are opened in current session (assuming it can get this information)
@techee: If you have no time to look into this, I might try to submit a PR myself. I'd just like to confirm first that this is not intentional and that there is no obvious blocker that would make this impossible.