SPOILERS AHEAD!
Ok here are the birthmarks explained (I'm putting the names in capitals for all the people we know have birthmarks):
JONATHAN had a birthmark. DIO stole his body and thus he got the birthmark. Every descendant of Jonathan has a birthmark, including JOSEPH, JOTARO, HOLLY and JOLYNE.
So back to Dio. Dio's bone transformed into THE GREEN BABY so it also had the birthmark. PUCCI merged with the baby so he got its birthmark. Because WEATHER REPORT is Pucci's brother, he also got the birthmark (somehow).
Because Dio was making children with Jonathan's body, all of them got the birthmark including: UNGALO (the guy in this chapter), RIKIEL and GIORNO.
When Pucci resets the universe ,IRENE also has a birthmark because she is Jolyne's alternate counterpart.
In part 8 KYO NIJIMURA has a birthmark because she is alternate universe Jotaro. YOSHIKAGE KIRA and JOSEFUMI KUJO have birthmarks and when they fuse into JOSUKE "GAPPY" HIGASHIKATA he also has a birthmark.
These are all the people in the manga shown to have a birthmark. Johnny was never shown to have a birthmark and Josuke from part 4 only had the birthmark in the anime.