The dimensions of maximized windows seem to get calculated incorrectly in dual-monitor setups.
Steps to reproduce:
1. Use a computer with two displays (I had this issue on a laptop with an external monitor connected) and arrange them vertically (workspace height = combined height of both displays).
2. Align the panels to the top and bottom of the top display.
3. Launch an application on the top display and maximize it.
4. Now align the panels to the top and bottom of the bottom display.
5. Open an application on the bottom display and maximize it.
I would expect the maximized window to occupy the area between the panels (display height minus 2× panel height). Instead, one of the panels overlaps the maximized window: either the one at the top of the bottom screen, or the one at the bottom of the top screen.
Currently on Ubuntu MATE 15.10 with all patches applied, but the issue has been around since 14.10. I've experienced it on two different laptops with a variety of external displays.
I never tested panels aligned to the left and right screen edges with the displays arranged horizontally, but this may present the same issue. Top/bottom-aligned panels with displays arranged horizontally are fine at least if they are on the bigger display (placing them on the smaller display may need testing).
PS: if this bug should be reported upstream, I will happily do that. (If there's some general guideline regarding whether a particular bug should be filed for Ubuntu MATE, upstream or maybe vanilla Ubuntu, a pointer would be appreciated.)
Can you test this using the Ubuntu MATE 16.04 Beta 1 live session and let us know if this is still an issue.