It seems that the bug with the items disappearing when picked up from crafting benches is back. I had it happen 4 times today after reintroducing the patch that was rolled back. I had it happen twice when I picked dung from animal cages and twice again when I picked specialized arrows from the carpentry bench.
Thanks for letting us know. I’ll see that it gets added to the player-maintained list of bugs.
If you’d like to report it officially, plese send a bug report to helpshift - Contact Us — Conan Exiles Help Center - which is the place for CEE bug reports so the devs can see them sooner.