Employment pass

I can understand hat you are in an emotionally difficult situation.
But unfortunately your post is difficult to understand as to what the actual issue is.
If the "vetting" (verfication of your background by external agency) was negative, it means that something in your credentials is wrong - or at least cannot be verified. In that case the employer should contact MoM (or the agency) to find out what. There might be an error or misunderstanding!
Your (soon-to-be-ex-) wife cannot influence all this. Your son (assuming he is Singapore citizen and lives at least partially with the mother) can in any case stay on in Singapore - and even for you, as father of a citizen, there are possibilities even if the work pass is eventually denied.

Thanks Beppi reaching out ,

Firstly MOM emailed my employer - saying they have been receiving  multiple callers on my behave on  employment pass application with my FIN and as well an immigration agency claiming I engaged them.

   My lawyer asked me to try to arrange a meeting with the MOM officer on my case  through my company and hopefully try to get agency name and those calling on my behave.

Secondly MOM mentioned they got a negative outcome from external parties. On my end I have no bad  records I know of .

3.The  Most troublesome situations is my troublesome relationship with local Spouse, inconsistent at ICA. Cancelling and reinstating my LTVP and false statements when ICA ask for clarification like  we are going through divorce. More I’m African, I don’t think it’s a reason but also not the best of reputation.

Just this week my lawyer and hers have come to an agreement for the divorce uncontested preceding to start on.

Yes I have a 3 years old daughter citizen.

What are other options for me to be here in singapore, my girl is my everything  ?

Honestly I’m just trying to understand if someone is trying to screw me up here with MOM call and others.

So someone called MoM claiming to be you, your employer or your agent?
That is a matter for the police, not MoM (what can they do about it???). Since you already have a lawyer, you should follow his/her advice.
As for staying on with your daughter, you should ask ICA which visa can be given for this - I assume an LTVP (not sure if you can work then, though).