There are two references to Jesus by Josephus. The first is the Testimonium Flavianum (TF), the one that gives us details about Jesus. You can go here and read Olsons paper on why it was probably added by Eusebius in the fourth century AD. Interestingly, Goldbergs paper (Goldberg, G. J. 1995 "The Coincidences of the Emmaus Narrative of Luke and the Testimonium of Josephus" The Journal for the Study of the Pseudepigrapha) suggests that part of the TF has parallels to part of the gospel according to Luke. Why Eusebius would do this is strange, so perhaps Josephus did reference Jesus in the TF, which was then doctored by Eusebius. If so, it would appear Josephus got his information from a Christian source, meaning the TF is not independent.
The second reference is to the brother of Jesus. When discussing people, Josephus usually mention the person being talked about first, followed by their relation to distinguish who he is talking about. The second reference does not follow this format, suggesting it was a Christian interpolation, probably before 248 AD, when Origen apparently references this passage.