They'll probably stay little.
However, try to make sure the minoxidil isn't dripping down your face if you're using the liquid. That might be part of the problem. If you're using it before you go to bed, try to use it a little earlier so it's dry before you go to sleep, it might be rubbing off your hair and onto your face more.
It's also possible that you are just developing some kind of unibrow as most males tend to increase in general body hair, but it does sound to me like it's being caused by minoxidil.
