There is also an opportunity to go into the transaction after it is completed and use the drop-down box to move all those items from the trade into your collection.
Just go into your completed trades under the transactions tab, find the trade in question and open it. Down at the bottom of the trade will be a status that says completed (check collection). Click on that link and you should see all the cards. They'll likely still be yellow. Use the box above it to move all in transit to collection.
I have had trades get "hung up" like this before but I never paid attention as to why so I just use that quick tool to put everything back in order real quick.
I hope that works for you.
---Ford