Geany 1.38, 2.0
In the editor right click menu, the editing functions (move line, comment line etc) act on the line with the caret on it, not the line clicked on. But the inserts (date, comment etc) act where the click happens.
This inconsistency is a footgun waiting to shoot, thankfully undo is available.
I can see why it happens, the things that are caret related are copies of normal menu items, which have no click position, only the caret. Maybe its as simple as right click moving the caret to the click position before calling the normal menu item.