(http://i68.tinypic.com/11gm7vc.jpg)
These are just leftover marks after explosives. They do not impact the game in any way. Essentially just decorations.
Yes, on mineral respawn near the explosive marks these marks will disappear.
Trees and minerals are not refreshed
Trees and minerals are not refreshed,Not just minerals
The minerals and trees should be respawning every 10-15 minutes if there are no players nearby (observing the spawn).
So if you're standing nearby they will never respawn there, but if you go away and come back in 30 minutes you will see respawned minerals/trees.
Also, what is the server name you're playing on? Is it an official server?
Community servers with low performance might experience resources respawning issue.
Regards!