How about some close up photos? Is it grafted or raised from seed please?
Don't know if this is relevant. If you see green leaves on variegated trees, it is most important to remove the green bits as they have more chlorophyl and if left on, the whole plant can revert to green. Logically, you probably don't need to worry. But if is grafted, it could have been grated on a tree stem originally with red leaves and stems. My observation only. I could be very, very wrong. If you don't want them, please remove them.
Before that, it would be nice to see some pics of your lovely Japanese acer!