Received 2- W-2s forms from the same employer

I received two W-2's from my employer that show two different incomes and amounts held out for two different states. One W-2 has the correct information in boxes 1-12, box 16 matches box 1 for the W-2 in the state that I worked in . The other W-2 has different amounts listed in boxes 13-17 in the state that I didn't work in with box 16 not matching the 1st W-2. I lived and worked in the same state for my employer for the Tax year. 

I've reached out to my company to correct the W-2. However I was told to go head and file using the W-2s. Won't this look like I made more then what was reported in Box 1 and won't I see a double tax?