Kirk could well have had it in mind, and already retrieved the Botany Bay materials. As stated, the trial seems to be just before letting them off at Ceti Alpha V. No one says they went directly there once Kirk defeated Khan in engineering, nor does anyone say that happened "Yesterday." It could have been several days later, with Marla already having been presented with her choice of court martial or exile, and voicing her decision at the trial. And that several days is or could be enough to go back for at least some of the Botany Bay materials, to be given to Khan once he's safely on the ground.
