One important point about an anomaly, taking the Multiverse Theory into account, is that it is not a naturally occurring phenomenon. As it does not technically exist within the physics of any given Universe, it does not necessarily exist in all realities/universes at the same time and can exist in a single universe. Perhaps Ensign Sue was confined to the Star Trek universe and upon her demise was released into all other universes. There are all kinds of theoretical canon explanations.