The difference is that the hard disk determined that some of the sectors could not be restored to normal state, they need to be marked as "bad" and should be never used in the future.
Generally when a weak / pending sector found, we can (regardless of software) "ask" the hard disk to re-verify the sector stability and depending on the result the hard disk can
- restore the weak/pending sector to normal state (so the amount of weak sectors decrease and no bad sectors at all)
- if the sector is physically damaged (so not reusable) then reallocate: replace with a spare sector. So then all future reads/writes (targeting the original bad sector) is redirected to the spare area, this is why the bad sector does not cause any further issue and the disk tests (regardless of software) does not show them.
This is completely independent from the software, the decision depends on the internal firmware of the hard disk drive.
Your hard disk probably had more weak sectors - from them, some are reallocated and some are restored to normal state.
This is completely normal and expected behaviour: as you can see, after the Disk Repair function of Hard Disk Sentinel, the hard disk is now stable, the read test does not show problems so ideally things are fine now. Now (as these are fixed and may be no longer displayed) you can acknowledge the 3 bad sectors to remove them from the text description and restore the health to 100%, to be notified about possible new problems only.
This is described exactly on Support -> Frequently Asked Questions -> How to repair hard disk drive? How to eliminate displayed hard disk problems?
and if you use Report menu -> Send test report to developer option, I can see the actual status and give step-by-step instructions.