An inconsistency Tolkien "solved" is most notably Glorfindel. The name was used twice in early drafts so he decided to merge those two persons even though they appears eras apart, and the first one had died. He did it by introducing the concept of reincarnation for the elves.
Whenever that kind if thing happens, a wizard did it.
No need to bring magic in. Tolkien might have made a mistake in translating the original Quenya, or perhaps there were transcription errors among the Noldorin scribes. Other histories have these same problems.