Yeh, you shouldn't find any items disappearing now.
The negative values there are just an artefact of the weight/vol of items changing and the calculated weight/vol capacity of cargo containers not being updated to match (in short: it's just an interface issue).
The items are probably just in an invalid state Rav. If you can get me the ID of the room where they were emptied and some information on the crates I'll take a look. Probably best to file a bug on it, I don't check these forms very regularly.