There's also a difference in the Labyrinth Zone - look at the ripple effect in the water on the Japanese version. It's not there in the US/Euro one.
Basically, as far as I know, Sonic came out in the US and Europe first, in a slightly "unfinished" state (presumably the team didn't quite meet the deadline), and the programmers took the opportunity to add the finishing touches before the Japanese release date.
What's odd is that Sega continued to ship the "unfinished" versions in US/Europe even *after* the Japanese version was released. I've never seen a US or European cart with the "finished" (Japanese) version of Sonic on it.