Income: Application vs. Verification Docs

How worried do I have to be if the HMDA reported income on the LAR matches what is listed on the application, but the W-2s, paystubs, tax returns in file do not support the income amount on the application?

You are supposed to report the income that was used. Can you locate that number in the file?

From the coversheet in the file, it appears that a third figure was used to calculate the DTI. So now I have one income figure listed on the application, a different amount evidenced from the tax returns/W-2s, and another amount shown in the DTI calculation.

This is where you have to determine if the bank has a standard figure they report on the LAR. It is supposed to be the gross income (but that doesn't always work, as you will find in a review of threads).
If the amount used in the DTI is an adjusted/net figure, what gross figure was used to arrive at that number? What is being used on other loans? You want consistency.

I would recommend in my report that the files must contain a clear statement of the gross income used for approval. This is important so that loan approvals can be compared for fair lending purposes. You want to make sure that all borrowers are being treated the same and not some having income adjusted and others not. HMDA is the gateway to fair lending for residential loans. Calculations are important.