I couldn't reproduce this issue, but I don't have actual HiDPI hardware, and playing with scaling with the GTK debugging tool doesn't expose this behavior.
Useful info I guess: * This icon is distributed by Geany (*geany-build*) * The *geany-save-all* icon (4th from the left) we also distribute displays fine * It is in the *hicolor* theme, whereas the *geany-save-all* one is from the *tango* theme. * We distribute the same sizes for all our icons, and a scalable version (so it's probably not we don't distribute a needed size) * The *index.theme* files look very similar (apart from *tango* not providing any *apps* category)