Mine had the same exact problem when I bought it. I pulled my cover thinking it was the gasket and then discovered those two little holes you are talking about. I think that those holes are there for a different water pump style and are not used on our cars. But they are tapped so deep and the metal is so thin on the backside of them that eventually they crack and coolant of course comes out. I fixed mine while the cover was off of the car with JB Weld two years ago and have never had a problem since then.
Like I said though I already had my cover off thinking it was a gasket leak, but there is no reason to have to pull the cover to fix it. Just clean it up realy really good. Maybe squeeze a bit of silicone in the holes then JB Weld over them and alow it to try overninght. You will be good as new for under 10 bucks.