We killed Levi in a group & it apparently didn't count for some group members.... We all -

Did damage after shields down
Stayed in the sector when Levi died
& we were all in a group.....

Idk about other people in group but for me & 2 more of my guild mates it didn't count the kill..... ¯\_(ツ)_/¯

Did you leave the sector and rejoin and not shoot it again?

I didn't leave the sector.