It's unprecedented for a Yonko and a Captain to have a lower bounty than his subordinate, they probably think Mihawk is stronger but Buggy is the brain. For all we know they might also think that Blackbeard and Shanks are stronger than Mihawk, I don't know.
Because Mihawk just joined Buggy unlike other Emperor and their underlings who were with them for a long time.
If the reason Buggy become Emperor is only because he make Mihawk his underling, he made him his inferior then its different than rest.
Buggy wasn't even a Emperor candidate or fifth Emperor, his rise to top was unusual than the rest so you can't compare Buggy situation with other Emperors crews.
As someone said above, its a comparable situation to Zolo beating Alber but still having lower bounty than Alber because previously Zolo had even lower bounty than Sanji, Buggy is similar to that as he wasn't even considered Emperor candidate he suddenly skipped all the steps and directly become Emperor unlike others.