Quran 5:117
I said not to them except what You commanded me - to worship Allah , my Lord and your Lord.
And I was a witness over them as long as I was among them; but when You took me up, You were the Observer over them, and You are, over all things, Witness.

John 20:28 "Thomas answered and said to him, “My Lord and my God!”

Considering the Quran is writing after the fact. Why didn't Jesus refute Thomas in verse 28 if the verse (5:117) in the Quran were true?

Quran 9:30
The Jews say, "Ezra is the son of Allah "; and the Christians say, "The Messiah is the son of Allah ."
 That is their statement from their mouths; they imitate the saying of those who disbelieved [before them]. 
May Allah destroy them; how are they deluded?

Being a Catholic, Jesus is the Messiah the son of God. But saying that...clearly I "disbelieved"