Another G.W. thing. Uber, this was a bad idea.

So I just got a sub-commander, and it said on the card that its favourite colour was purple.
It was the first time I ran into this so I thought it was just a little joke thrown in by the devs.
But then I saw it in-game and was very confused.

Once I realized what was going on I thought "Oh sweet! A real team commander!"
But nope, I couldn't control the units of this colourful cub-comm.

Now I don't dislike the idea of having colourful sub-comms, but if we can't control them it'd be nice if they couldn't be faction colours.
Just a thought.

That is actually a problem.

odd, they always showed up as white whenever i played with sub-commanders

This particular sub-com is purple; others are their normal color.

Perhaps a slightly lighter shade of your team's colour? Lilac in this case, if you are purple.

If not then as you suggest, simply a different colour.

More colours pls Uber.

Technical reason: this was a boss's subcommander, there are a lot more misc. subcommanders that use grey.

Yeah, it gets confusing. I'd like each subcom to have a different secondary color, which would be especially nice with Two Color Icons

No it wasn't, actually.
I got it from a random battle.

Yes, it was. All the minions are up for grabs at all times, so it didn't have to be boss battle.

But I got this before fighting any boss.
Unless you mean it just had the same name of the one I beat?

Even then, shouldn't it be an orange comm instead of a purple one?

Okay, "all minions" was a mis-statement; it should be "all your faction's minions" If you get a bunch of subcoms, you'll notice they are all Seeker or Acolyte as appropriate for your faction.

So, either your found parts for your faction's com, or the defeated commander was reprogrammed and renamed; the lore on this isn't clear.