more likely this took a place after all of them graduated/disappear as a process of being reincarnated. The girl singing (Iwasawa) was around episode 5 so I think this manga was more on the scene after Kanade (Angel/Tenshi) graduates. In the last scene where only Kanade and Yuzuru (guys with orange hair) left, between the two of them, Kanade was leaving behind Yuzuru as we don't know if Yuzuru stay behind until there a new student or he choose to graduate himself ╮(￣▽￣)╭
So I think the order of story was
Angel Beats! Heavens Door (Manga/Prequel before Yuzuru came)
Angel Beats! Last Operation (Manga)
Angel Beats! (Anime/Adaptation of Last Operation)
Angel Beats! Tabisuru Tenshi-chan (Sequel/Side story after Anime)
Oh i forgotten about it. There are ova or special episode something where Yuzuru become the teacher right? Anything possible cause the aspects of "time" and timeline kinda confusing here. And all that many theories about Yuzuru and his roles etc too.
Is this happened between the last scene in the anime? Where a girl singing something and the guy look at that girl? I don't read the manga version, but the anime become the reason i watch more anime. It so sad.