When I try to search for this problem I get many results, but most of them seem to be about mouse cursor themes, and I haven't played with that, and can't see how that could explain the symptoms I see.
When the mouse cursor is over a window from thunderbird, firefox or a (group) chat from pidgin, the mouse cursor is 2-4 times the usual size, that it has when over windows with xterm, liferea, pavucontrol, audacious or the friend list from pidgin (I think that's everything I have running right now). The exception being if pidgins task bar menu is open, then the cursor is the usual (small) size, no matter which window the cursor is in.
I use i3 as window manager with no desktop manager on debian Stretch (but I only upgraded a couple of days ago, and also saw the problem on Jessie).
Any explanation (and cure) or just hints to how I find out what is wrong.