For a grammar specification language (like XML Schema) to do a really good job, it really should also formalize how to specify error messages for that particular grammar. I'm not sure how hard it would be to do this, and I haven't seen any research on it.
An odd thing about XML Schema is that it's not very resilient - when this was supposed to be one of the cool thing about "extensible" XML. The next version is a little better at this. But it sounds like in your case, you wanted to get an error (because there was a real problem), it's just that you couldn't trace where it came from, or what its meaning was in terms of the system. It sounds like a hard problem. BTW: would using JSON or sexps have made this problem any easier? I think it's much deeper than that.