i think i might've glitched it since i can have sex with emma and she agrees to betraying mario but it won't say i visited him right under break katarina
If Emma agree with betraying Mario, then I assume you chose not to do her Sharing Route with Mario. You just have to progress with Sofia's Questline to arrest Mario in that case.
If the Questline still not dissappear from Logbook after that, it's just a bug. Just as same as when you choose to Betray Sofia, the Justice Questline still won't dissappear from the Logbook.