I have noticed the spoilers above the flaperon on the 787 extending, and the flaperon unmoving, when the spoilers are armed. The flaperons raise with the spoilers and spoilerons while the spoiler above the flaperon just slides with the flaperon.
The devs said they will fix it for a future update.
This is a known issue, it is hard to customize flaps for all planes. This is something we are looking to improve for the future:)