Not sure about where to post this or even if it's a bug/feature failure. But this scenario might light a bulb for people. I've noticed this developing two different stores where I've incorporated MMT tool usage quite heavily.

The example is simple. While customizing the PROD template I would incorporate the changes with an mmt push. I noticed the issue when I needed to include the content of some custom product fields. As far as I know, these need to be enabled in Admin in the Product Layout tab by moving the custom field to the active box. When I do this the template reloads to a previous version that didn't include the changes I just pushed.

The result is that you cannot "re" push the template. MMT cannot push the most recent change because the template had not changed locally. The workaround is also simple. In admin, you just need to reload the recent changes from the version history. (pro-tip: use good notes when using mmt push). As simple as it is the problem and the solution isn't obvious.

Maybe important to know is that I've only seen this on the dev stores in the case that this is a caching issue. I don't think there are any steps I am missing that cold avoid the problem, but that's also what I am willing to find out.