FiM: S9E8 "Frenemies"

[Al-1701]

I was thinking Team Rocket, if James was obsessed with body building.  Extreme body building.

Holy crap, you're right.   

Has Team Rocket ever tried to betray Giovanni?

There was the time they wanted to capture Drowzee and Hypno to put him to sleep so they could goof off without him knowing.  That's the closest they've come to outright backstabbing like what this Trio did.

As I said, this episode's resolution reminded me the most of Beast Wars' "Tangled Web".