I’ve used Alt+Print Screen for a long time and it always confined the screenshot to the exact size of the window in focus. Recently that is no longer the case: a certain border is visible around it.
Notice how my wallpaper/background is visible around the screenshot of the terminal window:
How can the original behavior be restored?
Perhaps unrelated, but I’ve noticed that for quite a while (since maybe Fedora 29?), the Connection Information window from Network Manager is not properly formed: it has a transparent area inside the right and bottom edges of the window:
It looks more like a theme issue (edit: or with the mate desktop spin)… I have tested in my fedora 30 with all default and could not reproduce your problem.