Chika Fujiwara calls Miyuki Shirogane as Miyuki-kun during the brief periods in s2 and the 1st live action that Miyuki isn't president. However, for the entire anime, manga and live action movies last I checked Chika calls Kaguya Shinomiya as Kaguya-san instead of, say, Kaguya-chan.
What I understand is:
Early on it's that Kaguya and Chika are the ones who are friends initially and then everyone else in the student council are just 'colleagues' with each other.
I guess this is seen in that they all call each other by last name, regardless of the honorific (shoki, kaikei, san, kun, senpai), except when they call Miyuki 'kaichou' and except Chika to Kaguya (and then apparently Miyuki too).
Given these I'd expect either Chika calls Kaguya as Kaguya-chan or that Chika calls Miyuki as Miyuki-san, Shirogane-kun or Shirogane-san. Instead Chika appears to afford more respect to Kaguya than Miyuki (san instead of kun) and has the same level of familiarity (both 1st name).
Question:
So why Miyuki-kun?
Guess:
Is this some joke related to how the times Chika has helped Miyuki eg volleyball, singing, etc like Chika is Miyuki's mom ? Here's what I read on tvtropes:
Fujiwara and Shirogane (...) odd mother-and-son sort of relationship (...) comes back to help Shirogane improve no matter how inept he is at the current subject. Moreover, Fujiwara started the manga with the utmost respect for Shirogane, but after seeing how flawed he truly is, now treats him only slightly better than Ishigami, which is more or less exactly what Shirogane expected to happen should Kaguya learn the truth as well.
I guess this would make sense. Chika calls Yuu Ishigami as Ishigami-kun. So, Chika would call Miyuki as either Miyuki-kun or Shirogane-kun. I think it's Miyuki-kun because they've become pretty close friends in the 1st season (while Yuu and Chika haven't really).
Maybe related:
Why does Naegi call Togami "kun" and Aoi "san"?
How relevant is gender in comparing last name-kun/chan compare to 1st name-san?