This is a bad situation to be in.
"We did not get an inspection, because my dad walked through and checked it out (he has been in construction for 30 years and owns property himself)."
Did he climb on the roof and check it out or just look from the ground?
"We just had a tenant tell us that they only replaces some of the outer section of the roof and that the middle has 4 layers."
How in the world is a tenant going to know if there are 4 layers of shingles on a roof?
"Needless to say, we need to get this figured out. I plan to call the seller and see what he says when I present this to him."
I would also ask if they have had problems with that particular tenant.
By the way I own real estate have owned real estate and will own more real estate. I can normally look at roof and tell from the shingles if a patch job was done or not. That said I am not a home inspector and hire one when I buy. Spread the liability a little bit.