Let's clear this confusion up.
John killed Benji
They hijack the car John was in.
They kidnap Patrick thinking its John
Patrick escapes.
Police recapture Patrick.
Flashback shows Elise and them taking Patrick whilst John emerges from the van.
Next it shows John had followed them to the shack and can see and hear them torturing Patrick.
John writes a note of apology, which makes perfect sense if you listen properly. saying things like, "I wouldn't be able to take the torture." etc.
John hangs himself and they find him hanging, it is NOT Patrick hanging there as Patrick did not have a bandana wrapped around his left leg.