TMZ Sports has learned ... the 39-year-old was being processed in Queens after allegedly hitting his 10-year-old son multiple times at the airport on Monday, when NYPD ran a background check and discovered an open investigation for misdemeanor assault in Harlem.

We're told the case stems from an alleged incident on March 13, 2020 ... when Ben is accused of getting in a heated argument with an adult female friend and grabbing the cell phone in her hand.

Sources tell us a scuffle ensued ... in which Ben allegedly injured the woman's finger and eye, causing pain and swelling.

The woman went to police and filed a report ... and the case remained open.

Shortly after Ben made bail at his arraignment in the airport case, he was then taken into custody on Wednesday and taken to the Harlem precinct for processing.

While it's another legal issue for Gordon, his attorney, Joshua Kirschner tells TMZ Sports he believes the former Bulls star's name will be cleared in the case.

"It’s very early in the case and we believe he will be completely exonerated once the investigation is complete," Kirschner says.