could you tell me what is the matter?这个说法对么？is应放在最后么？

准确地说，是没有这种说法的，你的这种意思是中国化的英语。
外国人一般说“能告诉我怎么啦？”的时候，
他们会说：Excuse me ,what's the matter?或：Excuse me ,what's wrong?

could you tell me what the matter is?

对的。和could you tell me what is wrong?用法一样

放在最后面,否则跟could 有冲突

不对,
could you tell me what the matter is?