How do i remove favorites folders from my ipad on ios 9.1?
I bet you're also syncing your iCloud bookmarks to PC and didn't think it was relevant.

I fixed this issue for myself earlier today by going into Chrome on my PC and deleting all the multiple "Bookmarks Bar" folders I found. It seems a new one was created any time a change was made in the iOS Favorites folder, and I guess when Chrome would then try to sync its own bookmarks back to iCloud, that's when it would create the duplicate folders on the iPad and iPhone.

If the issue comes back then I may just disable iCloud bookmark syncing on the PC entirely.