The Acharonim are bothered by 2 questions:
1. The Rambam (שופטים ט:ג) paskens that by the ב"ד הגדול we do not add dayanim, if so how can ר' נתן say 100 dayanim? How did they add 29 dayanim?
2. There is a din of אין ב"ד שקול so how can you have 100 dayanim?
The simple answer to the second question is that 100 is לאו דוקא, it is just a round number but it really was 99 or 101.
The מל"מ says maybe ר' נתן is talking about where they added שלא כדין however, he asks that ר' נתן learns his din out from a pasuk and it is very diificult to say that the pasuk is talking about where the ב"ד acted שלא כדין and he leaves it וצ"ע.
The Aruch Hashulchan answers that maybe we can be מחלק between הוראה and דין. In a case of דיני נפשות you can't have more then 71 dayanim and you can't have an even number. But maybe on איסור והיתר you can have more then 71 and it can be even.
The מהריץ חיות points out that the אנשי כנסת הגדולה had 120 members and it would seem that they were acting as the ב"ד הגדול.