Hi. I've just noticed a similar problem.
In my case, it worked for most of the mines that had finished, but it missed one of them.
I noticed it this morning (the game was running overnight). The mine's "target" appears to have been "full" at the point when it ran out of resources (i.e. the belt in front of it). Autodestruct had marked the neighbouring mines and belts for deconstruction, but it didn't want to mark the "target full" mine, even after I cleared the blockage manually.
Does that make sense?
Edit: I've just noticed another one that is exactly as the OP states, so the problem is not "target full" - that's just a coincidence. How do I send you a save on this forum?