[dumbluck]

The other thing I'm noticing is that some of these weird warp holes have the green square around them as if they were waypoint markers (which they're not--I certainly didn't set them up) and have a letter "M" in them at the bottom right corner.

That is a marker that you have encountered a minefield in that sector in the past. It doesn't just have to be around Warppoints, the marker can be put on any sector. You can even manually put one on a sector, even if there are actually no mines present. I think you have to remove the marker manually, too, even if all the mines are swept/used.