OK, it took a little digging, but I think I see what happened. It looks like the documents were uploaded but the "Save New Document(s)" button (lower left) wasn't pressed before the page was left. Mission Manager should have given you a warning, but it wasn't - that was a bug that's been fixed now.
Your files were there and using your allotted space, but since the Document wasn't saved MM wasn't showing them. The should be shown now. The reason the space was shown as being used, is the docs were really there. The space would have cleared overnight, as MM runs code at night that looks for and removes orphaned files like these.
Note: you might need to refresh the documents page (F5) to see the missing data loss warning.
Thanks for the report, let us know if you have any more trouble. Also let us know if you need more document space.