The first clip is through the viewfinder of me trying to use my EF 100mm F2.0 lens on my Canon EOS 60d. It just bounces back and forth around the correct focus point (too close or too far). This is in single shot AF mode. Eventually it locks, but isn't actually where the focus point is. Also while this clip is in poor light, the lens will do the exact same thing in broad daylight. Then I've attached what one of the photos came out as.

The second clip is using my EF 50mm STM on the 60d. A similar issue is occurring where the lens is jumping around the correct focus point. This is in continuous AF however. This lens often works much better and finds good focus. But sometimes an entire shoot will come out slightly focused too close or too far. The photo following is one example of how the lens focused too close (at f2.8).

Using an EF-S 18-135mm IS (not STM or USM) or the 55-250mm IS STM I have no focus issues. (As an aside, the 55-250 focuses all the way in an out while the camera is in image review for some reason). The camera does have magic lantern on it (pretty sure 1.1.1 version). However the focus issues persist even with a card that doesn't have magic lantern on it.

Has anyone seen issues like this before? Are my lenses broken or something wrong the body? Or maybe just expected performance?

Auto focus issues with EF 50mm STM and EF 100mm F2.0 on EOS 60D