Never expect to crack 100% of hashes.
To crack hashes, John the Ripper iteratively tries to input candidate passwords into the hash function and checks if there is a match. If it tries every word in the dictionary you provide it, or if it has exhausted the combinations you have set it to use without having cracked every hash, then naturally it will stop while there is still more remaining. All this means is that the remaining three passwords will need more time to crack, and that you may need to use a larger dictionary. This may mean a few more days, or the passwords may be so secure that it will never manage to crack them. This is to be expected.