[Colt]

So while trying to resolve an issue in FRED, I've stumbled across this. Apparently ordering a wingman, a wing or all fighters to "Disarm my target" or "Disable my target" will make allied warships refuse to engage said target. Just now I also discovered that ordering my pilot(s) to disarm enemy fighters will also make those enemies not targeted by the allied warship.

Here's a video of some testing I have done. There's more detailed text in the video itself.

[Cyborg17]

This is probably intended Retail behavior to keep beams from killing something you're trying to capture. 

[Colt]

This is probably intended Retail behavior to keep beams from killing something you're trying to capture.

That's... odd to say the least..

Like, what you said made sense. But I swear I've never seen this happen before. I've issued disarm/disable orders when I couldn't be bothered to find specific subsystems while dogfighting, and warships still engaged those targets. Or so I thought?

[Goober5000]

Yeah, this has been intended behavior ever since FS1.  In fact it became a particular problem for Wing Commander Saga, so karajorma coded a feature to work around it.  See this Mantis ticket for more information:

http://scp.indiegames.us/mantis/view.php?id=1956