The M.E tells Jake to look into the body to see the scarring on the liver, even though they extracted his liver earlier.
When Holt throws out his portrait, it is in a frame with glass covering it. When Santiago removes it later from the same garbage can, the glass is missing.
Oil paintings take several days to dry. If you touched it or even framed them on the same day they were painted, the paint would smudge all over.
Captain Holt wears his Commendation breast bar above his World Trade Center Breast Bar. When the WTC bar is worn, it is worn above all other medals, but below the American Flag bar.