There are a few here. When Ghastly vanished and appeared behind the group and Pikachu was trying to get Ash to turn around, but he didn't. He was a complete moron and kept looking in front of him, 80s villain-style.
I gotta say, when Team Rocket disguises themselves in obvious... disguises and the group can't figure out it's Team Rocket. What are you, stupid??? THEY'RE RIGHT IN FRONT OF YOU!!... Yet, they ALWAYS trust them on the off-chance that they're their 'good' twins...
Most of the 'epic' battles are too short. They need to have a long one, lasting for maybe three to five episodes with a huge twist in the end, instead of ending with TR 'blasting off' all the time, or the enemy turning good or something lame like that. Have them fight some ultimate enemy and something unexpected happening.
e.g. Pikachu fighting an 'ultimate enemy' and evolving into something other than Raichu, and on the level of Legendary! Something never before seen!!