Tax filing after H-1B Visa extension?

Hi ,

I applied H-1B extension last July but the visa expired on September before I receive approval. I kept working at the same company hoping my visa will get approved. And last month, I received the approval notice,finally.

The problem is that my salary until approval was lower than current minimum wages because my company was not sure if my visa extension will get approved or not.But I supposedly had to be paid more then current minimum wages which is about $10.000 higher than previous minimum wages.
Now Tax season is about to end and I’m wondering if I pay extra tax for last September to December. Or is there any other way to solve this problem?