According to the IEEE transactions information (tar file here contains IEEEtran_HOWTO.pdf along with the class files)
Axel Sommerfeldt’s modern and actively maintained subcaption.sty package  can not be recommended at this time because it does not provide an option to prevent the underlying caption.sty from taking control of main caption formatting away from IEEEtran.
Instead they recommend using subfig invoked like this
Are there any plans to add a
caption=false flag to
subcaption? It seems that
subfig has not been touched since 2005, so I would rather stick with
subcaption if possible.
EDIT: There is a workaround posted here, but it involves re-defining how captions should be formatted, which seems to partially defeat the purpose of using a supplied style file.