There's quite a bit, yeah. Trigun volumes 1 and 2 are the sketchy ones. Then Nightow had a publisher change, and the story continues directly on with Trigun Maximum volume 1. The English release by Dark Horse is currently up to TriMax 4, the Japanese is up to volume 12.

There were a lot of 'filler' eps in the anime that didn't come from the manga, and conversely there's manga stuff that wasn't put into the anime, especially in TriMax 2. But the two part company forever in TriMax 3.