I had v1.6.15 (I think) running, and it said that 1.6.16 was available, so I went to download the latest version, quit whatever was running, copied the new one over the old makemkv in Applications, and ran that. It appeared to be running fine, but it threw error after error (something about UNRECOVERABLE that I've learned means "your disc is scratched or seriously broken"). However, I quit makemkv, and noticed makemkvcon was still running. I'm not sure whether it was the old one, or not, but I killed the process, powercycled the blu-ray drive, and restarted makemkv and everything has proceeded just fine to the choose what to rip phase.
I believe this has happened before, both makemkvcon continues running after an application quit, and decoding errors after an upgrade which requires another app-quit and drive-powercycle.
PS: sorry, this should have been posted under the Mac OSX forum heading.