You could also say " Tell me what's the matter with it?". This song can help you to remember the sentence structure: https://es.video.search.yahoo.com/yhs/search?fr=yhs-arh-001&hsimp=yhs-001&hspart=arh&p=tell+me+what%27s+the+matter+with+you#id=4&vid=bd36a18743a6bb4428081475875fc603&action=click When we use indirect questions in English, those questions that are introduced by "Tell me..., Do you know..., Could you tell me...., ect...", we normally use the verb at the end. For example "Could you tell me where the station is" or "He asked me where I live". When we use the word WHAT we can say "Tell me what's the matter with it?" or "Tell me what the matter with it is?". The thing is that you can't separate the word "matter" from "with it" because "the matter with it" is like one single word, it's the subject. You can't use "is" in the middle! I hope this can help you.

Tell me what the matter is? Is an open question its not specific any answer could be the right answer. Tell me what the matter is with it? Is a closed question its referring to something specific, the answer can only explain the problem with "it" whatever it is.

Tell me what the time is Tell me what the time is in New York Tell me what the time in New York is Tell me: what is the time in New York? Tell me: what's the time in New York? Somehow it seems more difficult with the matter, but the structure and possible variations are the same.

I would say - 'tell me what is wrong with it' if asking about a problem related to a noun. A more general enquiry could be framed as 'what's wrong'/'what's the matter'.