I presume you are using middle click paste not `ctrl-c` `ctrl-v`?
Then see also #2629
Both #3310 and #2629 refer to the same Scintilla bug which has been partly fixed from what that discussion there says, but won't be further improved unless someone contributes the change.
I am not sure if the fix made it into the last update of Scintilla into Geany, and the person who last contributed a newer update unilaterally decided that they are so much more important than everyone else that they un-contributed (closed the PR and deleted the branch so nobody could use it) when nobody on the project had the time to review test and merge it in their personal time frame. [end gripe]