1) If they have applied using an NOC that wasn't eligible for CIC, then you have extremely good grounds for a complaint. This is something they should most definitely have picked up in the process.
2) Their is nothing they can do re the charges that were applied, as it's not something they deal with. Sadly, these notes are free if you apply yourself, but companies providing this service can charge what they like. This doesn't mean that they haven't ripped you off though, they did.
Once you lodge a complaint, it will be reviewed and the process will begin. You need to fill out a complaints form: http://iccrc-crcic.ca/AboutUs/public/complaintsDiscipline.cfm
My suggestion would be to stop using this consultant. Either do the application yourself with the help of me, CEC, iamtoby and everyone else, or use someone who is trust worthy. I can send you details of who I used to represent me.
They aren't necessarily required to give you the money back but the person I spoke to suggested that they may decide to do so when the process begins. If not, you can take them through the small claims court to recoup your money assuming the complaint has merit and AIMS are found to be in the wrong.
Their ICCRC number can be found at the top right of the AIMS website, you will need this for your complaints form.