This is likely an internal Gtk issue, not Geany. I believe it is often the fault of the window manager as many different Gtk applications cause the same output.
Agree its a GTK issue, but probably not the window manager, thats not part of GTK. Its more likely its to do with changes in the way GTK calculates its initial sizes getting silly numbers before the whole dialog is constructed and initialised. I know it changed late in the GTK3 cycle, but I'm not expert enough to know what changed.
It does no harm except being ugly, so perhaps the pragmatic approach is to leave it alone and if Geany ever goes to GTK4 it can be addressed along with lots of other stuff.
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