Big-Lipped Alligator Moment: In the anime, the treasure hunt episode ends with Nokoru and the Chairwoman staring at the Tokyo skyline during the sunset, just as the episode's enigma told them to do. However, while Nokoru is looking at the Tokyo Tower, he suddenly sees a somewhat deformed vision of the tower and is shocked for a brief moment before turning away and forgetting it. In ample context, it might be a premonition of the events in X1999, a manga in which an older Nokoru makes a cameo, but in this series it has virtually no meaning and is never brought again.
Ho Yay: In the manga at least, Nokoru and Suoh. Suoh knows every detail of Nokoru's life over the previous three years. Both boys are seen as loners to those who know them well, and the people around them initially express surprise when they take interest in one another. Physically, they could almost be seen as the template for many other CLAMP pairings - The tall dark (or blue...) haired guy with the shorter blond guy - sound familiar? Retroactively, the two draw some very close comparisons to Tsubasa -RESERVoir CHRoNiCLE-'s Fay and Kurogane, right down to the scene where Suoh holds Nokoru after he's been shot. It closely mirrors the aftermath of the Eye Scream incident in the Acid Tokyo arc. There's also a Say My Name moment, although not much attention is paid to it. Add to that the massive emphasis put on telling the story of how Nokoru and Suoh became friends, compared to the nods they give to Suoh's relationship with Nagisa. And of course, there's all that stuff about Suoh and the person who will determine his destiny. Suoh is very protective of Nokoru and talks about "staying by Nokoru's side" and "choosing to follow him" in a manner that suggests Nokoru is more to him than just a friend.
The fact that all the girls in the school drool over the three leads can be passable in some moments. The fact that the series shows the girls drooling over the detectives in literally every scene with them, on the other hand, not so much.
The decision to obscure the Chairwoman's face at all times can be understandable for copyright issues as mentioned in the main article, but it becomes unintentionally ridiculous when she is shown casually holding high her fan in the exact spot needed for just every camera shot.
They Wasted a Perfectly Good Plot: The conflict between Akira's identity as a master thief and his job as a CLAMP detective is barely addressed in the series, to the extent that his personal arc in the anime takes very twisted routes to ensure his partners never get to suspect anything of him - which leads to the question of why would CLAMP put an established thief character in a detective club series only to do nothing with him. A lot of people would have loved to see how the series explored this matter, as pitting the CLAMP School Detectives against 20 Faces for a battle of allegiances would ensure both drama and awesomeness. The feeling gets stronger with the mixed reception of the Idomu Yudaiji anime arc, as many believe that one focused on 20 Faces would have been a lot more powerful and appropriate to end the series.
Toy Ship: Kinda inevitable when you three cute and chivalrous grade-school kids out to help older women, and when you have two with canon love interests. The anime opening has hints of this too, in between Generic Cuteness.
Values Dissonance: Nokoru's repeatedly stated feminism can be a bit jarring for how easily it can be seen instead as a very Victorian paternalism towards females.