Most of these conflicts are between asteroids and natural satellites of planets, which are named according to different but partially overlapping schemes.
Later conflicts arose in relatively recent times from giving newly discovered satellites the same names as those of asteroids.
By this time, it was possibly felt that the true name of an asteroid such as "38 Leda" included its minor planet number, and so re-using the name for a satellite did not really create a conflict.
Some objects have names that refer to the same mythological character, but slight variations in spelling prevent there from being a technical conflict.
Some of the conflicts, surprisingly enough, are with planets and satellites, or other astronomical objects with long-established names.