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I cannot tell you what problem you are having at the Filipino embassy, but I doubt U.S. immigration will be there to grab you. They don't have the time or money to engage in that type of thing. So it is probably just a problem with your own passport that they want to resolve.
Here is the proof that if you do not have any crimes, ICE won't really be looking for you because you are not a priority to them. They don't have the money to deport everyone, so they are focused on those with crimes:
As far as your other questions, IF your marriage to a U.S. Citizen is real and not just to stay in the U.S., then yes, you can marry and file paperwork and your new spouse can petition for your son to come as a step-son and that process will probably take about a year after you become a Resident.
There is also the Humanitarian Parole that your son could use if he has a serious medical condition that cannot be treated in his home country:
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