With these many inconsistencies, and with Starfleet personnel constantly tampering with the timeline, I have come up with my own hypothesis - these inconsistencies are the result of the timeline changing.
For instance, in 2364, there was a starship Atlantis
with the registry of NCC-72007. Then, between "The Neutral Zone" and "The Measure of a Man", the timeline changed, and now there is a starship Atlantis
with a lower registry. The people are no more the wiser for they change with the timeline, but, we the viewer, are aware of the changes for we exist outside their world and are looking in.