The bars displayed for PvP moves are extremely misleading and you should never pay them any heed. I can't think of any other game feature to date that was so bad at providing useful information.
As for the actual question, Thunder Punch became more expensive to be in line with Ice and Fire Punch, other 3-bar moves didn't have changes to their energy costs. In addition to that, Thunderbolt and Flamethrower also cost more now to be in line with Ice Beam.