Hi, I can confirm that this occurs on the latest MacOS and Anytype version. It looks like the fundamental issue behind this is that the toolbar icon is always set as the system dark/light mode and not the background color.
I am still not satisfied with the icon color in toolbar. When switching to dark mode, the icon turns white which is good. But for all the other apps i use, the icon is white all the time. Why not do the same for Anytype? I really don’t get it.
White all the time makes sense to me because it creates a uniform look and does not cause a bug when having an app in fullscreen. See screenshots, they are both in light mode. No matter which app i open in fullscreen, toolbar turns black and therefore icon “disappears”.