It's clearly a well intentioned mistake, but it's the kind of thing that can bite you later because someone will accept the license and use it for something you never intended. At that point it's a really big headache.
It gets even more complicated when people try to mix licenses that are incompatible -- it works fine until somebody challenges it. At that point it's an absolute pain. The last thing you want on your project is to have someone say they are going to sue you because you don't have permission to use their code. It's really, really important for people to follow the licenses correctly and GitHub is in a wonderful place to help with that. It's a win for everybody. I would say even if people realise that they can't use GPL for some project because it is incompatible with the license for other code they are using, it's better than going for years and having a problem!