Most likely the man had some of his issue magazines (post 94) marked "Restricted Military/Law..." after he retired. Got caught with them. Was made an example.
Not sure if this is fact or not... But i do belive if the magazines were made prior to 1994 that they were legal under the bans NY had in place, prior to the newest laws.
You are correct, the preban (normally unmarked mags) were good to go. I was stationed in Ft. Drum from 96 thru 2000.
This is my personal experience.
I had friends who were locals and members of the Watertown Sportsmans Club - so I shot there often.
Being by Drum...a major active duty Light Infantry Division....peoples tastes tended to go towards the EBRs. Even with the locals. Before I got stationed there - my friends had plenty of high caps. They may have picked up one or a dozen once I showed up...who knows.

One guy literally had a duffle bag full. Very, very few were "restricted". All came from Drum. It was jokingly referred to as overflow.
Many times Law Enforcement on duty would would show up at the range to shoot. They never bothered us and many times would chat. With my haircut - I was obviously a "Drumie" as they would call us. But the other guys on the range. No way were they military. Tons of AR's w/ mags piled all over the place. And not just my buddies. No checks. No hassles. No problems.
Once one of the shooters had a couple restricted mags on his bench. He was down on the other end and clearly wasn't with me. A cop taps his finger on the guys mags, chuckled, and said be careful. No checks of the AR's to make sure that they were correct Pre or Post configurations for their receivers. Guess that culture has changed.
Honestly it was a nightmare to enforce the NY state laws in that area prior to this last law passing. Forget the locals. 10th Mountain Division. Infantry guys love our modern auto loading weapons. We came from all over the country with much less restrictive laws. We'd bring our weapons with us. Most of the laws were too confusing or difficult to comply with so we didn't. If they were easy to follow....the majority of us wouldn't have anyway. They were all bubblegum laws. At the time in NY - to legally own a pistol, you had to have a CWP. Your pistols were listed on the permit. They were registered. I saw tons of soldiers with pistols. Most kept off post or at friends places. No permits.
At the time in that area the laws simply were not followed. The cops didn't check...because they didn't want to confirm what they already knew. Locals or "Drumies". Again...guess times have changed. They made an example. Good luck with people complying.