Hi Elounmeloun,
I was reading back on your post and realized there were some additional updates on the forums that you may not have seen regarding issues reported. In the link I posted above - [Known Issue][PS4/XB1] Crafting Menu Reset / Story Items Locked - there was a workaround found for crafting the story items that remain locked in the crating menu. If you use the quick crafting menu you should be able to craft the story items. It may be easier to do if done directly after defeating a boss, or in the boss area. If it is not showing up in your quick crafting menu, you may also wish to try emptying your inventory and moving away for all crafting materials to see if it prompts the option to show up.
The team confirmed the binoculars issue will be fixed in the next update, however we do not have a date as to when that’ll be released yet.
Regarding the missing items from crates, there is an issue that results in any spoiled items becoming stuck in crates, and upon reloading the game all items in the crate can vanish. There is unfortunately no workaround for this, but any further updates will be posted here: [Known Issue][PS4/XB1] Spoiled food stuck in crates - I’m not sure if this is exactly what happened in your save to some of your items, but it has been reported by a number of player’s missing items since the last update and I wanted to ensure you were aware of it.
Unfortunately the PlayStation trophies themselves still have no workaround and I believe this is tied to the issues with the main crafting menu remaining locked.
This may be all information you’ve found from being on the forums, but in case not, I hope the information provided above may be of some help to you. And as I mentioned in my other comment, I will pass the request for an information update onto the team.