Has anyone else run into issues with secondary market loans not being accepted by Fannie/Freddie as a QM because the fees they charge put the fees put the loan over the tolerance for QM status?

They only thing we can do in this situation is cover the fees with the rate, resulting in a higher rate to the customer. Maybe the GSEs should look at reducing their fees!

I do not understand your question. Why would you think secondary market loans and loans salable to Fannie/Freddie have anything in common? What fees are you specifically referring to that are being charged?

We consider Fannie/Freddie as secondary market loans, so those are the loans I am referring to.

Some of the additional fees they normally charge (in addition to their .25% market condition fee which they charge on all loans) include:

DTI/LTV (low DTI and high LTV)
Cash out fees
Condo fees
Investment Property fees
Secondary financing fees

Some of these can add up pretty quickly and go over the 3% threshold.

We consider all of those delivery fees when offering rates to customers. If something changes after initial disclosures are done, we then usually charge that fee to the borrower.