Incorrect amount of free space on 2009 Macbook
You appear to have a heavily-used computer with a 5-year-old drive. I would be more surprised if it didn't have issues.

Two things you can try:

Step 1. Clone your drive to an external drive using something like Carbon Copy Cloner. Do NOT use block copy mode or Disk Utility, that copies the problems as well.

Step 2. Boot from something else, like the clone, reformat your internal drive and clone back (you can use block copy this time).

If that doesn't solve the issues, your drive has hardware problems. Replace it with an SSD and your issues will go away, plus you will get a huge speed increase.