I have two W2's. (My full-time job and Marine Corps Reserve income)
I also have a 1099 from my current employer before I was hired.

I have no issue filing these, my question is this.

No taxes were taken out of my 1099. So when I file this 1099 they take 85% of it from my refund. Is this normal?

For example: My refund with my 2 W2's are $2,000 (example). My 1099 is for $1,100(example) when I submit my 1099 my refund drops to $1,200. Essentially they're taking $800 back from the 1099.

This is money I worked for as a contractor and they're taking a majority of it from me.

I know nothing about taxes so I am unsure if this is normal...

Thanks

You must report all the income. On 1099-misc income, you will pay SE tax at 13.3% plus income taxes.
1099-misc (nonemployee compensation) income: You are self employed or independent contractor. You will report your income and business related expenses on schedule C or C-EZ (Form 1040). Then you put net income (or loss) on line 12 of Form 1040. This income is subject to SE tax at 15.3% (this is shown on line 57 of Form 1040). Even though schedule C treats you as a self employed, which may not be correct for you, this is how you report this income.
Your U.S. Tax Return: Tax Filing by Self Employed Sole Proprietor or Independent Contractor (http://taxipay.blogspot.com/2008/04/tax-filing-by-self-employed-sole.html)

So is taking $800 back from an $1,100 1099 normal. Essentially that made me working at $4/hr after it was all taken out...

No, $800 is on high side. Your 1099 for $1100 should drop your tax refund by income by around $300 to $400.

That's what I thought. Is there anythign that can be done about this?