When you update a repeater field, it should delete the entries in the database. Did you see the deleted entry on the backend? Could you please check if the entry at fault in the database is different from the others? It’s possible that the entry is duplicated somehow.
Also, could you please check if your code is the one that caused this issue?
Welcome to the Advanced Custom Fields community forum.
Browse through ideas, snippets of code, questions and answers between fellow ACF users