You know after thinking about it since I was reminded of it, I think the hate of Team Rocket in this episode is unfounded.
Well look at BW006, Team Rocket were on a mission, and the Twerps interfered, almost in the exact same way as this episode.
Team Rocket were minding their own business doing what they were doing when the twerps got involved.
This isn't like BW030 where Team Rocket went out of their way to specifically capture Axew, Pikachu (though that failed), and Druddigon. They had a plan to catch the Cottonee from the beginning and wanted to catch the Cottonee, and then when they found the "colony" of Cottonee, the twerps were there and "interfered" of course it didn't really matter considering it was the Cottonee that foiled Team Rocket's plan.
So again I think the hate of them in this episode is unfounded, for the simple fact they had a plan to catch a lot of the Cottonee, and not be messed with. Unfortunately as it goes, the twerps were getting themselves involved with the Cottonee themselves.