On my Fedora system, the minimize, maximize/restore, and close buttons look strange (almost like overlapping/cell-division style) in certain apps such as Gradia, Spider, and Extension Manager. I’m using a custom “traffic signal” window control theme (macos-titlebar-main), but not issue with all apps.
In order to isolate the issue, could you check if this is reproducible with the default icon theme?
Also, is there anything different with the apps that have the issue, e.g. installed as Flatpaks, whereas the other packages are installed as RPMs?
Are the preinstalled GNOME apps (e.g. Files, Text Editor) looking as expected?
For some reason, in your screenshot Spider looks like a legacy GTK app, even though looking on flathub.org it appears as if it was developed using libadwaita. Do you know why is that? Maybe share a screenshot of the Files app, and of Gradia.