If they have issued you Form 16A then in that case they are not treating you as employees they are treating you as independent professional so yes if you have filed ITR 1 and shown salary income that's incorrect.
You must check your contract.
You can choose to file ITR 4 and show 50% as income if you are covered under the criteria.
You can revise it till 30.06.2020.
If you are a doctor you can shown your income under 44ADA.
If you need any assistance feel free to contact.
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