When I was underwriting, I was a DE underwriter and ANY negative amounts/returned checks, was grounds for a turn-down.
You should be very, very concerned, b/c it demonstrates that he/she is spending every dime they have, and if they are going UP in payment (rent vs new mortagage payment) that is at high-risk for first-year default.
Just remember the first-rule of FHA....protecting the buyer...too many underwriters forget that and Loan Officers treat FHA like it's an alternative to subprime...that isn't what FHA was designed to do.
If you had to do a manual underwrite for 'another issue' then you now have TWO layered risk factors.
That would get a thumbs down from me.
I would prepare the customer now that it could potentally kill his deal.
The underwriter is probably going to turn it down for that reason b/c if FHA won't insure it after it's underwritten and closed, that is the MOST expensive buy-back that a lender makes, so if you can't justify it 6-ways to Sunday, no way, no how. That is in ADDITION to HUD keeping a rating on the underwriter that will follow you with any lender, when you have DE loan authority....no underwriter is going to put their job at risk like that.
PS: You can't do a verification of deposit (VOD) form on an FHA...for those that don't know...not allowed. Full bank statements, all pages, must be in the file.