What state are you in? A husband and wife LLC in a community property state can be treated as a disregarded entity, which is what you have been doing. If you are not in a community property state, a husband and wife LLC has to be treated as a partnership, and has to file a Form 1065 partnership tax return.
A pass-through entity is not the same as a disregarded entity. (That might be what confused you.) A partnership is a pass-through entity, not a disregarded entity.
Community property states are Arizona, California, Idaho, Louisiana, Nevada, New Mexico, Texas, Washington, and Wisconsin.
I found out because we did a 1031 exchange and had to fill out the W9 as a partnership.
If not, the IRS was almost certainly never expecting an income tax return (Form 1065) from the LLC and exactly what tax ID number did you enter on the W-9?
Regardless, if you did not hold the interest as community property in a community property state, you might want to consult with a tax professional, in person.