To reproduce this: have two files open in separate editing panes (split vertically, for example). If you select a word in one pane, you can immediately use the middle mouse button to paste the word in the other pane. But if you select an entire line, by clicking on the line number in the margin, the X selection is not updated, so if you middle-mouse paste in the other pane you will still get whatever was the last X selection.

Explicitly copying with Control-C or the like is a possible workaround. But it should not be necessary.