Percy and Thomas are very close friends, but that does not mean they are not prone to having a falling out from time to time! Other than that they still remained best friends despite a few bumps in the road.
After the events of Thomas and the Magic Railroad, Thomas didn't really like Splodge. During the events of "Splatter" however, he and Gordon got back at Splatter. Presumably hours earlier (in "Dodge"), he told Dodge what to do, annoyed that he wasn't paying attention.