The use of the figure of speech could be different. It depends on the context again. I would use it to describe a situation or a behaviour as being quite lame. E.g. My husband has asked me to go to Egypt with him. He is going to get a personal loan to pay off the expenses. Well, I doubt I will go. There are too many holes in the roof. (I mean when we return who is going to pay? Me! Out of MY POCKET, Never :)) Hope, it helps :)

It means the idea you have, or the situation you are in, has a lot of problems and you need to think of a better answer. If you leave holes in a roof, your house will fall down due to rain and animal damage.

I didn't know it was a metaphor. What happens when you have holes in the roof? That should answer your question.