Do you know which parts of Seafoam island have Kabuto? I’ve checked every bit of water I can access but no luck.
I've sat in every body of water in the cave and seen an Omanyte in all of them.
The waters that are assigned to Kabuto might not be accessible, I could only find 2 areas and both spawn Omanyte. I just modded the files to make Kabuto spawn in the water where you can catch a special Pokemon at Seafoam Island. I'm not sure if this makes Omanyte impossible to catch (I'm too lazy to test)
https://www101.zippyshare.com/v/hyUOt5yQ/file.html
Just replace the old files. This is the 151 Pokemon version btw