I'm posting here on the advice of sasschary, who was helping me with this problem in the "Am I Infected?" board (located at: https://www.bleepingcomputer.com/forums/t/649245/malwarebytes-anti-ransomware-and-msys2-false-positives/)
As a brief summary of the problem, whenever I have tried installing and updating MSYS2 as of lately (6/13/17), either MalwareBytes is interrupting the MSYS2 update process, causing the installation to break and render it unable to delete unless rebooted (pacman.exe ignores my administrator rights), or pacman.exe is going into super-administrator mode on its own, breaks the installation, and then MalwareBytes flags the action. Either way, any time I've tried to run MSYS2, I get a notification of ransomware on my computer, but MalwareBytes is unable to scan or move the file. What should I do?