Did you get a chance to look at your paystubs to see if they were withholding taxes and paying their share of self-employment tax? If they were, then go back to them and ask why they sent a 1099. However, since you received a 1099, the income would be subject to self employment tax.
The good thing is that you can deduct some expenses you had related to the job. A W-2 job would not allow you to do that. I am attaching a link that has some common expenses you may use. Take a look and see if any apply.
common business expenses