Your file will be okay, since you send them at the very early time. They will receive it before they start processing it.
Scan your passport again with all the marks/stamps again. Upload it through CSE asap because they can reject your application if they figure it out.
You need to read the INSTRUCTION clearly on CIC Website for IRAQ PCC. They basically have instructions for all the PCC.
http://www.cic.gc.ca/english/information/security/police-cert/mid-east/iraq.asp
Do I need to provide a police certificate for Express Entry?
You do not have to provide a police certificate from Iraq unless we ask for one.
When you apply for permanent residence, you will be asked to upload a police certificate.
To submit your online application, write or type "As per IRCC instructions, I do not need to submit a police certificate from Iraq with my application at this time" on a blank piece of paper and
upload it in the Police Certificate section.
If we ask for a police certificate later on, you can upload it at that time.
We will not accept police certificates sent by mail for Express Entry applications.