I had a theoretical look at this:

Mint-Y-Sand theme uses the Mint-Y-Sand icon theme
Mint-Y-Sand icon theme inherits from (in order): Mint-Y, Adwaita, gnome, hicolor. It provides very few icons itself
Mint-Y provides more icons, but doesn't seem to provide everything we use, including e.g. neither gtk-new nor document-new.

Thus, it falls back to Adwaita for those. So everything seems normal, except that Geany shows more icons than this theme was really meant to.

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