Here's what I'm seeing, when I send scouts to a pirate planet to destroy mines, on beta 2B:

1.  As soon as the scout arrives at the pirate planet, the auto-attack toggle is set on even if it was off before the phase jump.  Right clicking does not disable auto-attack (i.e. no way to disable it).

2.  If the scout jumps to a non-pirate planet, the auto-attack toggle works fine again.

3.  On pirate planets, reveal mines ability doesn't do anything -- i.e. even when activated, the mines are still invulnerable.

I'm fairly certain this worked fine on beta 2a.  I also haven't tested this with advent scouts, or mines on non-pirate planets yet.  Specifically, this happened with TEC Loyalists picked by Random, on the map Secrets.