We need to investigate this deeper, please email us the issue description along with the technical data http://kb.parallels.com/9058 to cs(at)parallels(.)com, so we can check it for you.
I made a clean install of OS X 10.11.3, then I updated Parallels Desktop to Version 11.1.3 (32521) and then I installed OS X 10.11.4 - that works for me. Mouse and Keyboard works.
I made a clean install of OS X 10.11.3, then I updated Parallels Desktop to Version 11.1.3 (32521) and then I installed OS X 10.11.4 - that works for me. Mouse and Keyboard works.