Rebuild the directory of your Time Machine (HFS+) disk with DiskWarrior and you will be shocked.
On the other hand, APFS may get corrupted, but so far the only tool to fix it is Apple Disk Utility - First Aid. Start repairing from bottom to top. In other words, repair APFS Volume, then Container (partition) and finally Disk. If it fails at some stage, try again in such stage, because sometimes it requires several trials to fix it.
Once fixed, repair the next stage up, and so on until the disk ,as said above.
Hopefully, DiskWarrior 6 to rebuild the directory of APFS disks will be released soon, once Apple releases Time Machine 2 to backup into APFS disks (now it is only possible into HFS+ disks with Time Machine 1.3), APFS becomes mature that way, Apple releases full documentation about how to write to APFS, and then developers like Alsoft can use such information to release DiskWarrior 6, as said.