"Do you know where _is_ it?"

This was a mistake I had seen a Japanese learner of English make. In fact, I notice that with subordinate clauses that begin with question words (such as "where" or "what"), a lot of Japanese learners of English will switch the verb and subject like they would in a question, though it is not. It's like they're generalizing a rule way too far. I wonder if this is a result of harmful explicit grammatical instruction.

What could be causing this?

Well, I can easily see where confusion like this comes from. They simply don't know that "where" is functioning differently in the two questions, particularly considering that they're both questions. Considering that subordinate clauses work COMPLETELY differently in Japanese than they do in English, it's an understandable mistake.

- Kef

But if they had enough input, they would clearly see that that is wrong, right?

Unless perhaps they had the pattern reinforced by incorrect usage before they received enough input.

furrykef,

Probably they might have had some input or teaching by a teacher and took it too far too fast, and forgot to look at how subordinate clauses are formed. In fact, I think figuring out how to form subordinate clauses and connect them to independent clauses is the most important part of learning grammar. I imagine that every language makes use of such things, and that is the one thing that causes the brain to start to want to tap into it (otherwise it would be nonsense such as "flying spaghetti monster frying pan wallet").