<p></p>
<p>This directly depends on the GTK icon theme used, which can be configured like the rest of the look & feel in your setup -- which you didn't mention BTW.<br>
That's not something Geany controls, it just requests an icon with a specific name (<em>close</em> would be my guess, but I'll have to check), and get whatever image the icon theme has for this.</p>
<p>It looks like the icon theme you use changed that icon in a manner you don't like.  You can then either change icon theme, or change that specific icon (it can be overridden in <em>~/.local/share/icons</em> IIRC, details TBD).</p>

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