Almost certainly those other charges were heresy, simony (buying and selling of church offices), and perpetuating the Western schism. These were considered more serious crimes because of their religious nature.

But that answer alone is incomplete, so let's have some context. Antipope John XXIII was born Baldassarre Cossa in the kingdom of Naples. His father was the lord of Procida and Cossa himself became a soldier. However, he later switched paths and instead studied civil and canon law and then entered into the service of Pope Benedict IX. He became a cardinal in 1402, but remained more interested in living like a warrior than a clergyman. Two of his brothers were executed by Ladislaus of Naples for piracy and Cossa himself was accused of collaborating with robbers and highwaymen, which he sometimes used as muscle to rough up his rivals.

Now, it's important to explain here that from 1378 and 1410, there was something called the Western Schism. This meant that there were at least two popes both claiming ultimate authority, one in Rome and one in Avignon. This occurred, in large part, because from 1309 until 1376, the papacy had been based in Avignon. This situation had arisen because of conflict between Philippe IV of France and Pope Boniface VIII, but remained in place for so long because Rome had become awash in bloody violence as a result of the Guelph-Ghibbeline wars. In 1376, Pope Gregory XI decided to return to Rome on the advice of Saint Catherine of Siena and then died shortly after. After his death, Italian cardinals in Rome elected the Italian Pope Urban VI while the French cardinals in Avignon elected the Frenchman Antipope Clement VII. This situation continued for years with there effectively being two popes, one in Avignon and one in Rome.

In 1408, Cossa and six other cardinals withdrew their allegiance from Pope Gregory XII on the basis that he had broken his oath not to create more cardinals without consulting them. In response, Cossa and the other cardinals met with cardinals from Avignon to attempt to resolve the schism. They declared the Pope Gregory XII and Antipope Benedict XIII were both deposed and elected Antipope Alexander V. But Gregory and Benedict refused to resign, so now there were 3 popes. Alexander died a year later and thus, this group of cardinals elected Cossa as Antipope John XXIII.

Cossa's most formidable enemy (because he was very nearby) was Ladislaus of Naples. In 1413, he assisted Louis II, duke of Anjou in his abortive attempts to remove Ladislaus as the king of Naples. After that failed, Cossa fled to Florence where he met Holy Roman Emperor, Sigismund, who hoped to end the schism once and for all. The result was the Council of Constance, which Pope Gregory XII also authorized. The council decided that all three papal claimants should resign and a new one should be elected instead.

But Cossa didn't like the results, so he fled from Constance in disguise with the assistance of Friedrich IV, Duke of Austria. Sigismund was enraged and declared that Friedrich was to be deposed as Duke. Ludwig III, Count Palantine eventually caught up to them, though, and convinced Friedrich to hand Cossa over.

Cossa was then taken back to Constance where he was accused of a whole host of crimes and imprisoned. He was eventually freed after the Medici paid his ransom and submitted to the authority of the newly elected Pope, Martin V, who made him a cardinal bishop.

Now, the $64,000 question is, "Was Cossa actually guilty of all the crimes he was accused of?" The answer is, "Probably not." That he was a shady customer is not disputed, but even shady customers aren't guilty of every crime.