Lets see, I few things I found (that may or may not be intentional?)
1. The Warps on Island 3 and 7 to Birth Island and Navel Rock have an invisible wall block in front of them.
2. Lorelei on Island 4 acts as if you beat the Rockets, but their sprites are still there (although not able to be talked to).
3. As a result of #2, you can't go in Dotted Hole to finish the Sevii Sidequest, get Mewtwo, etc.