M5 + EF 100mm f/2 focus issues

You should be getting some decent results from the M5 with almost all lenses, with one exception.... The Canon EF 100mm f/2 USM lens is a PRE-DIGITAL lens released in 1991.  Canon themselves said that they do not recommend the use of "Pre-Digital lenses" on modern digital cameras, especially on the Mirrorless R-System models, but presumably also on the mirrorless EOS M-System. Quite a few people do use them, and they appear to work.  Many pre-digital lenses work just fine on the M/R system bodies.  But this is an issue that will continue to surface.  In addition, this particular lens was known to have some AF issues in the past, though not the one you described.  In the cases I'm familiar with, this lens would sometimes stop focusing at a certain distance and it sometimes stopped Autofocusing altogether.  There's even some self-repair videos on YouTube on how to get them going again when this happens.
.
The reason Canon give for not recommending Pre-Digital lenses on modern digital cameras is because pre-digital lenses (usually anything manufactured prior to 2002) tend to be made with a very different metering in mind, were subjected to the effects of UV light (modern sensors have a UV deflection layer) and use a different method of Auto Focus, especially prior to the DPAF sensors.  Canon also noted that the lens coatings on older lenses are prone to affecting the Auto Focus.  The older USM motors used in the earlier lens designs from the 1980's are on your lens and I assume that they might not be able to keep up.
.
In the case of this rarely encountered lens, it's probably going to produce problems similar to the one you've encountered.  You'll notice that your Sigma lens isn't problematic with AF because it's a much more recent lens design with modern optical coatings.