I think the prevailing theory about why Greg Scarpa Jr. was put into the "Rat" category was twofold; there are some street guys who believed, at the very least, that as a son, who was also extremely close to his father on a daily basis, hung around him constantly, as well being as a street guy himself, who was a member of his father's own crew, who became a made guy no less, over such a lengthy period of time (many many years, decades, in fact,) Junior would have, or should have, "smelled" a rat (so to speak, no pun intended.)

The fact that he supposedly never did... became suspect in some wiseguys minds. And it became hard to believe that he never "allegedly" questioned his father about it? Or if he did think something was afoul, he never brought those suspicions to the Colombo brass as he should have...It was a bit too much to swallow. So Greg Jr., was also considered a rat by some. Who, at the very least, turned a blind eye to it, making him complacent in his father's scheme, (If he wasn't downright part of it as the time passed.)
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The second incident which made some guys label him a rat (which I personally, do not agree with,) was after he got that lengthy sentence for heading the Staten Island-based drug ring and was doing his federal time.

Either by happenstance or previous design (in a deal worked out with the feds beforehand,), Greg Jr. was housed with a guy who was known as a Middle Eastern terrorist, and the two prison inmates became friendly. Over a period of time, Scarpa got the guy to open up to him in confidence (thinking Scarpa was a devout mafioso, a stand-up guy.) The terrorist admitted committing criminal acts, terrorist acts, against the United States of America. (I don't remember if Scarpa tape-recorded the guy or not.)

Scarpa promply brought the information he obtained from the guy to Federal Authorities and they used whatever evidence Scarpa provided to arrest and prosecute the Middle Easterner for "terrorism." Scarpa may have also testified in court (I really don't remember.) But at the very least, he was debriefed, spilled the beans, was recorded, and provided pivotal evidence, helping the feds make the case.

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PS: Now I think there are many wiseguys and street guys who really don't give two shits if Scarpa helped take down some terrorist degenerate plotting against America. In fact, after experiencing what we did in New York City after the horrific terror attacks of 9/11, I suspect that there are some wiseguys who would (openly, or privately) applaud and give him a medal for such a thing. Looking at his actions as a completely separate thing from "organized crime street activity" and making an exception in this case regarding "keeping quiet" regarding law enforcement. Some mafiosi might even view it as an act of heroism and patriotism for America, similar to the actions of mafiosi back in Sicily and Southern Italy during WWII, when the Mafia bosses in certain villages and towns aided the Allies in landing on the Island of Sicily, providing them with scouts, interpreters and other logistical support in their efforts to defeat Adolf Hitler and Benito Mussolini and the Axis Powers.
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But, overall, these two factors played into Scarpa Jr being labeled a rat. A third incident which I'm sure didn't help his cause was when he had the physical altercation and punched out Lucchese boss Victor Amuso in jail, after Vic had called his father a rat. Collectively, all these factors effectively sunk Scarpa's ship!

I hope this answers your question.