Most significantly, there is another Jesus in the retelling of the stoning of James, the brother of Jesus "called Christ". The story goes on to say that King Agrippa replaces Ananias (the high priest responsible for James' stoning) with a priest named Jesus son of Damneus. Others have noted this, and have argued that Jesus son of Damneus was orginally meant to be the brother of James in that story. Following this assumption, the "called Christ" bit, similar to the Testimonium Flavium, would be an interpolation by a later redactor.
Now, Jesus son of Damneus' reign as high priest was fairly short-lived; he lasted only two years. And who was he replaced by? Another Jesus. This one called "Jesus son of Gamla". That presents us with three notable men named "Jesus" in very short order.
1. Jesus, brother of James (alleged Christ)
2. Jesus son of Damneus (high priest)
3. Jesus son of Gamala (high priest)
This should probably make you raise an eyebrow at least, but admittedly, it could just be chalked up to chance. Unfortunately, however, that's just the beginning of the Jesuses.
At the same time that these two successive priests named "Jesus" were in power (c. 62 to 66 CE), yet another fellow named Jesus proved notable enough for Josephus to mention; Jesus, son of Ananias (as in the former hight priest, Ananias?), a "husbandmen and plebeian" (not a son of the former high priest, I guess). For those unfamilar with the "woe, woe to Jerusalem" story, this Jesus is described as follows:
But, what is still more terrible, there was one Jesus, the son of Ananias, a plebeian and a husbandman, who, four years before the war began, and at a time when the city was in very great peace and prosperity, came to that feast whereon it is our custom for every one to make tabernacles to God in the temple, began on a sudden to cry aloud, "A voice from the east, a voice from the west, a voice from the four winds, a voice against Jerusalem and the holy house, a voice against the bridegrooms and the brides, and a voice against this whole people!" This was his cry, as he went about by day and by night, in all the lanes of the city. However, certain of the most eminent among the populace had great indignation at this dire cry of his, and took up the man, and gave him a great number of severe stripes; yet did not he either say any thing for himself, or any thing peculiar to those that chastised him, but still went on with the same words which he cried before. Hereupon our rulers, supposing, as the case proved to be, that this was a sort of divine fury in the man, brought him to the Roman procurator, where he was whipped till his bones were laid bare; yet he did not make any supplication for himself, nor shed any tears, but turning his voice to the most lamentable tone possible, at every stroke of the whip his answer was, "Woe, woe to Jerusalem!" And when Albinus (for he was then our procurator) asked him, Who he was? and whence he came? and why he uttered such words? he made no manner of reply to what he said, but still did not leave off his melancholy ditty, till Albinus took him to be a madman, and dismissed him. Now, during all the time that passed before the war began, this man did not go near any of the citizens, nor was seen by them while he said so; but he every day uttered these lamentable words, as if it were his premeditated vow, "Woe, woe to Jerusalem!" Nor did he give ill words to any of those that beat him every day, nor good words to those that gave him food; but this was his reply to all men, and indeed no other than a melancholy presage of what was to come. This cry of his was the loudest at the festivals; and he continued this ditty for seven years and five months, without growing hoarse, or being tired therewith, until the very time that he saw his presage in earnest fulfilled in our siege, when it ceased; for as he was going round upon the wall, he cried out with his utmost force, "Woe, woe to the city again, and to the people, and to the holy house!" And just as he added at the last, "Woe, woe to myself also!" there came a stone out of one of the engines, and smote him, and killed him immediately; and as he was uttering the very same presages he gave up the ghost.
Putting aside this Jesus' obvious similarities to the Biblical Jesus, let's take a moment to put him in context. Josephus tells us Jesus of Ananias first went to the Feast of Tabernacles four years before the war - in 62 CE. He also states that Albinus was procurator. Albinus took power immediately after the stoning of James; thus, James must have just recently been killed at the time Jesus of Ananias enters the scene.
So taking all this into account, one might infer that this Jesus was the previously mentioned brother of James. Angered by the murder of his brother, he traversed to Jerusalem to ceaselessly condemn it, screaming at the top of his lungs. It's odd, however, once one considers that "certain of the most eminent among the populace had great indignation at this dire cry of his, and took up the man, and gave him a great number of severe stripes."
Why is this odd? Presumably, the high priest (very likely one of these 'eminent people' or 'our rulers') at that time was also named Jesus: the son of Damneus - who was already mentioned as a potential contender for being the brother of James. Even more bizarre is that "Damneus" seems to be a nonsense name - the Latin literally translates to "Damned" in English. So Jesus son of [not the recent high priest] Ananias is damning Jerusalem, while Jesus son of Damned is high priest.
Now, apparently, Jesus son of Ananias doesn't end his charade until the war breaks out in 66 CE. At that time, he gets killed in a somewhat comical fashion. Before the war, Jesus of Damneus/Damned had been replaced with Jesus ben Gamala. This Jesus (Joshua) ben Gamala is described in the Talmud as marrying Mary (or Martha), daughter of Boethus (Yebamot vi 4). While Josephus once indicates him to be the son of Gamiliel, he otherwise refers to him as "Jesus son of Gamala"; though Gamala probably refers to the stronghold near Galilee, rather than to a person: https://en.wikipedia.org/wiki/Gamla
Additionally, a number of Jesuses are described as leaders on the battlefield. The most notable of which is Jesus son of Sapphias, who is described as being: one of the high priests, the leader of the Galilean city Tiberias, and the leader of a number of mariners/fisherman and poor people.
In addition, a Jesus son of Shaphat is described as leading a group of bandits near Tiberias; and sometimes a 'Jesus' is referred to without any identifiers in Wars and Vita.
So, to summarize, from the years 62 to 66 CE, we have:
1. Jesus brother of James (alleged Christ, relevant in 62 CE)
2. Jesus son of Ananias ("woe to Jerusalem" omen, 62-66 CE)
3. Jesus son of Damneus (high priest, 63-64 CE)
4. Jesus son of Gamala (high priest, 64-65 CE)
5. Jesus son of Sapphias (a high priest, c. 66 CE)
6. Jesus son of Shaphat (leader of bandits, c. 66 CE)
A number of other Jesuses are also mentioned, but most considerably pre-date the aforementioned figures. A 'Jesus brother of John' was killed by John around 180 BCE; a 'Jesus brother of Onias IV' became high priest in 175 BCE; a 'Jesus son of Fabus' was removed by Herod as high priest in 23 BCE; and a 'Jesus son of Sie' briefly replaced Eleazar ben Boethus as high priest in 3 BCE.
So what's my point? Certainly, that something strange is going on here. I've noticed that none of the individuals called Jesus are ever identified separately in the same section - though I might have missed an instance of this occuring. Is it possible that Jesus #1-6, ever-so-elusively, refer to the same individual?