Hmm, be careful, there are two issues going on here. When we see just one, Close button, that by design.
Gnome desktops don't have the minimize and maximize buttons on any windows any more. Its because they think too many things like buttons will confuse their users. So, on Gnome, its only ever the Close button.
I found that all the KDE/Plasma show all three, Linux Mint showed all three using Cinnamon with XFCe. So, I added Mate to the Linux Mint install and when running Mate, no buttons !
So, no question its a Mate or at least upstream of where we play, issue !
In my app, its rare that I trigger the situation, I have just added a standalone Close button to that (for this release) but I think its needs chasing one way or another.
Davo