In the Boruto manga, Boruto got a curse mark for killing/defeating an Otsutsuki clan member (Momoshiki). Why did Naruto not get a Mark for killing/defeating Toneri?
Naruto didn't get a curse mark from any Otsutsuki because he has never killed one before.
In Toneri's case, they fought, and after some time, Toneri decided to stay on the moon and atone for the sins he commited. He is also shown completely alive and well in the Boruto anime until Urashiki froze him in time.
Now with Kaguya, it's kinda the same reason. They didn't kill her, but instead sealed her using Rikudou: Chibaku Tensei. Over time, when shes longer in the seal her chakra is sealed as well. This is why her Rinne-Sharingan deactivated the minute the jutsu went into play.
Naruto never killed Toneri, didn't kill Kaguya, but instead sealed her.