Normally the Pirate tries to take the most efficient, straight line, intercept course to a target. If for some reason it figures out that it's not possible, then it does its best by simply heading towards the target itself.
This can definitely happen when the Pirate is already headed towards a target and the opponent hires a Navigator, increasing the speed of the target.
Unfortunately I have also seen it happen in other cases (like this one probably). It looks like there's a mismatch between the speed calculations when launching the Pirate and when actually executing it. I'll be taking a look at this over the next few days and release a fix in an upcoming update.