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OK then I guess we're back at why this penalty is showing, since the expenses are greater than revenue. W2 is fixed withholdings throughout the year, so not too sure what else could be. 

To test where this might be coming from, I removed the income from the business and when going back to the 

Underpayment Penalties screen, the penalty amount is now a bit lower.. Does this mean the underpayment is from multiple income streams?

Could it also be from Investments and Savings section?