I'm using Geany 2.0 on KDE/Plasma 5.27 and have been facing annoying issues with the caret position. In some cases (I have not quite yet found the minimum steps to reproduce it though from a fresh start of Geany), the caret will either disappear altogether, or the text will not scroll to the correct position.
One typical way it happens is when scrolling multiple pages (so that the caret gets out of view) and the clicking in the document to place the caret in the new position. When the issue arises, when clicking on the new position, the document will scroll back to the previous position of the caret. It doesn't usually happen until Geany has run for a while. Again not sure what exactly triggers it, but when that starts happening, it keeps doing that until Geany is quit and restarted.
Likewise, when doing searches, if the search has reached the end of the document and we agree to keep searching from the start of the document, then the document will not scroll to the position of the found occurence, but will stay where the caret originally was, and the caret disappears.
I'm not sure exactly how to give more information than this. It's easy to reproduce after a while in my case, but the minimal steps are not obvious (except that it eventually happens after some use.)
I had a similar issue with Geany 1.38 before upgrading to 2.0, so it's not new to the 2.0 version (but was kind of hoping it would fix it).
I have the "project organizer" plugin enabled, if that could make a difference.