I have a pending deposit than is dramatically less than the amount given to me, I did not select any special options and IRS said it shows that FULL amount being sent.

You can see what you were charged for. Click on Tax Tools from the Menu on the left side in your return. Click Tools then My Fees. This will give you a breakdown of any charges.

This link will provide more information on the Refund Processing Fee.
https://ttlc.intuit.com/replies/3301372
You can track your refund with Santa Barbara Tax Products Group.
https://taxpayer.sbtpg.com/login