Good question. The grammar rules are not different.
This is correct: "Could you tell me what the time is?"
This is correct: "Could you tell me the time?"
This is wrong: "Could you tell me what is the time is?"
In each case, there is inversion of the auxiliary verb "could" and subject "you". The "what" clause is the object and is therefore structured as an embedded question, not an interrogative question.
The "I wonder" statement is not grammatically a question, even though in practice you are questioning yourself.