Basically, the only things that have a carrying limit are weapons and consumables. You can either drop them or put them into your duffle bag at shelters. The only things that can not be dropped are flashlight and hook. Turn the option off, put them into your duffle bag, exit the item screen. There should only be one of each in your bag now. If you somehow managed to break the total item limit of the game, just start dropping all the stuff you don't need and also empty your duffle bag and drop those things. Then exit the game and reload your save. Items should be gone.
Update: Check the steam forums. Seems to be a bug, nothing related to the trainer.
[Edited by madatcheats, 2/19/2016 6:02:52 AM]