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Watched a stream and saw a Dondozo use Order Up against a mon using Protect. The Stat Boost effect still happened even though the attack failed against the Protect.
Haven't been playing all that much, but haven't run into any major glitches. Camera ones and the choppy framerate of people, Sunflora and windmills are all I can think of.
I think if your mon is standing around, you can hit the right bumper while facing a wild mon to target it for attack. Or it might be too weak to attack.