Settings > Tools > Scene Duplicate Checker shows that scenes have missing pHash, but you already ran the generate task on all scenes.
This is most likely due to files having some kind of corruption. Due to the nature of file hashes, missing or corrupted data can affect the hash value, so if any errors are encountered, pHash won’t be generated to avoid creating an invalid hash.
[!note]
Those files might still be fully playable as media players ignore most errors during playback.