Greg Cox wrote:
It's also possible that Khan met Chekov shortly after the events of "Space Seed," but before Khan's people were dumped on Ceti Alpha V. In To Reign in Hell, I made a point of establishing that Chekov was among the crew members who escorted Khan and his people to the planet and provided them with supplies, said goodbye to Marla, etc.
The simplest explanation has always been that Chekov was already a member of the crew during Khan's takeover, just not assigned to the bridge yet.
IIRC, Vonda McIntyre suggested a friendship between McGivers and Chekov in her novelization.
ST II also features Mr Kyle on the same ship as Chekov - and Marla and Kyle have an encounter in "Space Seed", in which she bails him up at phaser point.
Walter Koenig says that, on ST II, he realised immediately
that Chekov hadn't met Khan onscreen in TOS, but worried that if he mentioned something the writers might give away his coveted lines to George Takei (not thinking that Sulu hadn't been onscreen with Khan either.) Maybe John Winston should have done some lobbying.