The record is not clear about whether Trump knew about this specific overture, but it is known that he has discussed pardons many times with staff and also in public.
The million-dollar question here is why was this done? Was it done out of compassion? Or was it done in an attempt to thwart the criminal investigation lead by Robert Mueller into the President and his associates?
Legal experts quoted in the article differ as to whether Trump's lawyer and possibly the President himself could face prosecution for obstruction of justice if there was evidence the pardon offer was made to shield criminality by others. Nonetheless, some say yes.
One of the indicted individuals, Michael Flynn, who was a campaign official and Trump's first National Security Advisor, later plead guilty and has been cooperating with Mueller's investigators. The other indicted individual is Paul Manafort, Trump's campaign chair, who has been charged with conspiracy against the United States, conspiracy to launder money, failure to file reports of foreign bank and financial accounts, being an unregistered agent of a foreign principal, and false and misleading statements to federal officials.
Whether or not Manafort accepted a pardon offer is not known. Unlike Flynn, he has not plead guilty nor is he cooperating with prosecutors.
Of course, if Trump pardoned anyone, and that person accepts the pardon, such an action legally is equivalent to admitting the criminal charges are true. More dangerously for the President, that person could then be compelled to testify against Trump or anyone else because the Fifth Amendment would no longer apply.
The article doesn't mention if this issue was ever raised by Trump or his attorneys.
The most important issue raised by all this is glaringly clear -- is this something an innocent man would do? If Trump did nothing wrong, why would he try to stop a criminal investigation into his actions -- wouldn't an innocent man want to clear his name?