It sounds like the inventory bug that has been reported by numerous people (including myself), where an item can’t be smuggled in with a briefcase or to an Agency Pickup. And with large items that can’t be smuggled into Hidden Stashes, it effectively means they aren’t available to use at all. (Which items you can’t smuggle seems to vary greatly from person to person.)
Unfortunately, I don’t think there’s anything you can do about it except report it to the bug thread or open a ticket with IO support, but I still can’t smuggle in a handful of items.