It shouldn't do that. You can have as many bookmarks for the same
webpage as you want (although I can't really think of any reason why
you would need two bookmarks for the same webpage).
Something isn't working properly.
It could be the bookmarks preference file has become corrupted. Try
quitting Safari, then copying the file Users/{your user
name}/Library.Safari/Bookmarks.plist to another location (e.g.
downloads) and then deleting it, then restart Safari and try adding
your bookmarks again. If it works, then the old Bookmarks.plist file is
corrupted.
If you're using iCloud syncing with another device, then that could be
the potential culprit - turn off the syncing and see if the problem
still happens.
You could try saving the second bookmark to a different / new
sub-folder. If that works, then maybe you can use the Edit Bookmarks
option to move it to where you want it.