Here's
my 2011 list of all the TOS references that were snuck into the comic:
Now, it could be that these items snuck through because they were minor enough continuity details that Paramount's licensing people missed them. But perhaps it's significant that it's only general concepts and supporting characters that got used, not specific episode plots or central guest characters. Compare it to DC's first TOS comic, which had an unrestricted license and did many plots that were direct sequels to TOS episodes or brought back central guest characters:
It's not every case, but most of the DC stories brought back major guest characters or directly followed up on story threads from TOS episodes, which is something none of the earlier Marvel issues did.
So maybe the restriction on Marvel was that they couldn't use
storylines from TOS, rather than a blanket ban on
concepts from TOS. What they did use was generally just worldbuilding details or minor characters. So they could mention cordrazine but not Edith Keeler, and could use a cloaking device but not bring back the Romulan Commander. Although that doesn't fit with Mike Barr's comments in that article linked to above (where he says, for instance, that they weren't sure they could have Spock perform a mind meld until they remembered it had been done in TMP).
I think the "sneaking" explanation is pretty likely, though. The comics never came out and said "Look out, it's the Klingon stasis weapon from 'More Tribbles, More Troubles'!" They just included these characters and elements without attributing them. And back then, before Memory Alpha, it was harder to keep track of every last bit of episode trivia from TOS. So the approval people might've skimmed over "Admiral Fitzpatrick" or "Berthold rays" without recognizing it as a reference.