The Shulchan Aruch (Y.D. 349:1) prohibits benefiting from a cadaver, whether Jewish or gentile. However, there is extensive discussion in the later authorities regarding gentile cadavers, and many maintain the prohibition is only rabbinic or even permit it if the gentile gave full, informed consent before his death. Therefore, a number of prominent authorities permit use of gentile cadavers for the purpose of medical training or research in the stated conditions. (See Nishmat Avraham, ibid.)
Thus: If you do not know whether the phantom you are using contains bones, you can rely on the majority of phantoms that do not.
Even if you know that the phantom contains bones, you can still follow the likely majority that the bones are from a gentile cadaver (unless known otherwise), and rely on the authorities that permit medical usage.