It can mean one of the following: - they don't agree with each other. - they are confused. - they are out of sync. It's basically saying, "We aren't on the same page here". Might also have several other meanings, but these are all that I am aware of.

It means to be confused, think something else to what the person is actually saying http://www.urbandictionary.com/define.php?term=crossed%20wires