I am so sorry for replying so late.. I just checked the forum now
The reason for returning was because I have attached a very old IELTS report (2008) for my wife instead of the one she did before immigration. So I think they considered it as a missing document in the file
As for checking the file, it seems they check the documents before proceeding with the acknowledgment. My form and my daughters were stapled with all the related documents and stamped as "Complete" (I think that was the word), and my wife's form was stapled with a letter on the top mentioning which document is missing (IELTS).
Let me know if anyone has any further questions