I started playing the Mercenaries standalone scenario and I believe I've encountered a bug. After a while I ran into a pirate base. I figured I'd better blow it up, but when my fleet arrived, I found I couldn't attack it. After many tries, I decided that maybe the pirates aren't enemies in this scenario. However, a number of turns later, a fleet of five tiny pirate ships destroyed one of my ships. So then I tried attacking their fleet, but I couldn't attack that either. They can attack me, but I can't attack them. I've found two more pirate bases, so I assume this will eventually be game breaking when they're swarming all over with stronger ships.

At this time I'm not sure if this is limited to the Mercenaries scenario since it's the only thing I've played so far with 1.6.