I had this exact same problem. I finished the game and had 283 orbs. I spent 10 hours of in game time using multiple guides for in world orbs, and there were none, so I can only assume it was a faulty side mission. Luckily I had a previous save file from right after I completed the game when I only had 228. I used the orb glitch demonstrated in the video above to get one extra set of three orbs, and then I went through and did the last of the side missions *again*. When I got 286, the trophy DID pop. So yes, use that orb glitch once, and continue on with the game. I would also advise you to NOT do an orb hunt side mission, so leave one for the last thing to do in the game, so that just in case it happens you can have the opportunity to do the glitch again.
Also, when you are doing the orb glitch make sure you have two identical save files before attempting, because if you are too late, the game will auto save and you won't be able to do the orb hunt again.
Hope this helped! It sure drove me crazy for a while.
Alright then that's three witnesses! I hope I have an orb hunt left over... I might...
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I'll be sure to check this out later. I'll add the video soon.
i believe the different methods include punching then restarting mission before you hit the orb and jumping over the orb and then restarting the mission, after restarting jak will still move towards the orb and sometimes get it, not fullproof though