Conquest: Order 66 won't count?

Same. I gave up on and and EA Help did nothing. My guess is the coding. This has happened before where it's kind of like the enemy inflicts it upon themselves, so it doesn't count as your characters inflicting it.

But the weird things is that it counted it twice but not all of the other times I did it 

Same here. I was doing fight on Padme squad, so one O66 was due to Snips cleansing Scorch and additional one with CX-2 hitting GK. At some point those Scorch inflicted just stopped counting.

I've got the same issue this Conquest.  It counted twice and then never again.  It is getting cleaned off by clone troopers.  It is the last points I can get to the get the red crate and I'm going to get totally messed over by it.  They want us to spend money, but can't be bothered to fix their game.

It's the same reason why DR's Deathmark from his leadership doesn't count toward the Deathmark feat. In Scorch's case, technically the enemy inflicts O66 on themselves. You need to apply it with your own active abilities, meaning you need to hit them three times with CX-2. It is a dumb as bricks clause in my opinion, but it is consistent with what's been done with conquests feats before (the DR Deathmark thing; Caustic Emissions dots don't count towards "inflict dots on enemies" feat because the disk makes the enemy apply dots to themselves, it's not your characters doing it).

Just skip it and find something else to use for points.  They didn't fix it after the first round, they won't fix it for the final round because it'll be gone after next month.  Unfortunately, that's CG's apathetic response all too often with events like conquest, datacrons, etc.