I'm not an admin but I think you are ok. Most of the subway passes under unclaimed land and any ore under your area is yours by right. The only way I can see you getting into trouble was if you destroyed the tracks, flooded the tunnels, or damaged the subway in general. The very fact that you fixed the holes you made and told us about it just shows that you care about the work of others and are an honest player.I have a confession to make.
I was in my house and was mining downwards at an angle when I eventually came out in a long corridor with some coal on the floor and some gold ore on the walls. "Strange" I thought, I was in desperate need of some coal at that point though, so I began mining it out. Then I decided to explore and wandered further on down the corridor when I finally discovered that it was in fact part of the subway
I then ran back to the hole I made in the floor, filled it up with what stones I ad on me. Then went back to the way I came in and filled that in as well.
So in short, sorry for stealing the coal, I didn't know
Please don't ban me..