First Aid found corruption for repair but First Aid from Recovery did not solve the issue

I am trying to solve this problem on my Macbook Pro 2012, running Sierra 10.12.1. I've run First Aid from Recovery and did not find any corruption, everything was fine. I've run it again from my OS and I still get the problem as follow:

Verifying storage system
Checking volume
disk0s2: Scan for Volume Headers
disk0s2: Scan for Disk Labels
Logical Volume Group 04B93861-2D39-432E-A393-50AD1CE83BFE on 1 device
disk0s2: Scan for Metadata Volume
Logical Volume Group has a 24 MB Metadata Volume with double redundancy
Start scanning metadata for a valid checkpoint
Load and verify Segment Headers
Load and verify Checkpoint Payload
Load and verify Transaction Segment
Incorporate 0 newer non-checkpoint transactions
Load and verify Virtual Address Table
Load and verify Segment Usage Table
Load and verify Metadata Superblock
Load and verify Logical Volumes B-Trees
Logical Volume Group contains 1 Logical Volume
Load and verify 55E94947-EFBC-473A-A314-5EBEFF0A949A
Load and verify F9FAD274-A819-4CDC-9F05-F519DA8DBED2
Load and verify Freespace Summary
Load and verify Block Accounting
Load and verify Live Virtual Addresses
Newest transaction commit checkpoint is valid
Load and verify Segment Cleaning
The volume 04B93861-2D39-432E-A393-50AD1CE83BFE appears to be OK
Storage system check exit code is 0.
Verifying file system.
Using live mode.
Performing live verification.
Checking Journaled HFS Plus volume.
Checking extents overflow file.
Checking catalog file.
**Incorrect block count for file processing-3.2.3-macosx.zip.f0fd203b-064b-4fd7-bce4-89d8c693971e**
**(It should be 6452 instead of 28451)
Incorrect block count for file USB_LUCA.zip.40b230dc-a016-4312-afcd-c1a087fcd8a2
(It should be 4630 instead of 530384)**
Checking multi-linked files.
**Incorrect number of file hard links**
Checking catalog hierarchy.
Checking extended attributes file.
Checking volume bitmap.
**Volume bitmap needs minor repair for orphaned blocks**
Checking volume information.
**Invalid volume free block count**
**(It should be 19383016 instead of 9221304)**
*The volume Macintosh HD was found corrupt and needs to be repaired.*
File system check exit code is 8.
Operation successful.

Anyone had the same issue?

When repeated attempts to repair the filesystem fail, your next step is to back up all the files that you need and erase the partition.

Set up a new filesystem and then re-test the repair in recovery. If that fails - your hardware needs repair. If that succeeds with a clean check - you can set up a new account and/or restore from backup.

Live repair is not to be trusted, but live errors are of concern. I would try a verify in live mode to be sure you have issues before going to the erase / re-partition step as that can take some time so you'd rather be sure before starting down that path.