Are you saying that the son is nominee for the Trust, so the income reported to his SSN should have been backed out on his 1040?  Who is the trustee, anyway?  Are there other beneficiaries?  Did the father have any good reason not to let the son just inherit the assets with no strings attached?  Or was he just a Stubborn Old Buzzard?  And did the broker make a mistake, or did the son misinform them?

One problem I see is where the trust's capital gains are taxed.  If the trust gets around to filing a 1041, are the capital gains assigned to the trust (as state law often requires), or to the beneficiary?  You could have a situation where the trust now owes tax, but the son gets no refund because he is in a zero tax bracket for LTCG and qualified dividends.  Or, the trust could pay less tax on the same income - although this is unlikely. 

I suspect that if the whole story were known, you wouldn't want it to be known here.