“Are they trying to get me into trouble or get them selves out of trouble?How are they able to fill out a tax form for me when there is nothing stating I worked there?”-----> Sounds like your ER trying to avoid paying taxes, I mean Soc Sec taxes. You're only a contractor if you are able to complete the work using the tools you want to work with, using your own methods, on your own time/schedule. It is also completely the wrong way to handle these types of payments. You'd really have to have separate sets of duties and conditions for the 1099 work than for the W-2 job. If your ER incorrectly classify you, an EE, as an independent contractor, your ER can be held liable for employment taxes for you, plus a penalty.
Please visit the IRS website:
Independent Contractor (Self-Employed) or Employee?