FYI for some of those participating in this thread, lest you incur confusion in the future: "burn" means to write data onto the disc. "rip" is what MakeMKV does, copying data from the disc to your hard drive.
I am having a hard time believing that this is just a one-off issue considering I'm having the exact issue. Every single other BluRay rips with no problem besides The Martian. I'm on my second copy and having this exact issue so if its a defective disc and/or BluRay drive...that just seems to coincidental to not have something about this movie be the culprit.
That said it sounds like plenty of folks have had success so its rather odd..
Not with CloneBD, since the initial problems would first show up in anydvd with decrypting issues since it's only been released today. And since CloneBD doesn't decrypt,... You do the math.