matlab -nodesktop causes java processes to appear in dock

I recently started to try to use Matlab within emacs, which launches matlab by matlab -nodesktop. Once I did this, most of the time when I launch a java process, it now shows up in the Mac Dock and there is an icon with a black M and a read A in the Mac toolbar at the top of the screen.

My normal workflow often involves have a dozen or more java processes running, so this floods the toolbar and application switcher with icons and applications that I never want to switch to. I have rebooted and the icons/applications remain.

Is there a way to revert this change?

I am using matlab 2015a and MacOS 10.10.5 Yosimite.