Resetting the SMC usually fixes that problem.
Try unplugging your Mac from all power and leave it overnight. Sometimes that will reset the USB ports. The USB ports on portable Macs (MacBook and MacBook Pro models) can not handle a large amount of current draw for any length of time once the warning is displayed on the screen. Protection kicks in and shuts the ports down.
Chances are they shut down before any damage occurred but you should let Apple look at it anyway