Hi there, I'm the programmer so I might be able to help you. I'm guessing the problem occurs in battle?
There should be a button in the middle of the screen saying "Start Battle", which, when pressed, will have the enemies move around. Then when the button "End Turn" pops up, you should be able to left-click a pirate to select them and then command them around.
Outside of battle, you should only be capable of talking with pirates, with no enemies being present.
If this doesn't help with your problem, may I ask what operating system you're using, and maybe get a video/screenshot of the problem?