no problem at all. in fact it likely means healthy activity going on. the surface of my scoby almost always rises above liquid. i just keep a coffee filtre over the top of my 4l jar to keep feeding it air without too much airborne debris. never once had mold or contamination. kombucha is very resilient
actually i fill my jar right up to where it starts to narrow, knowing that the scoby will bubble and bulge up. i do this under the assumption that i am creating a little more of a seal around the edges of the scoby, thus trapping more natural carbonation in the brew.
Here's what mine used to look like under a constant 26C-28C aquarium heated brew in a conical vase. It looks this way because it's a much warmer ferment than room temp. Now I use a 4L pickle jar at room temp. Less tedium until I can go continuous ferment. I read somewhere that 26C'ish is ideal for a healthy balance of yeast and bacteria growth. It's not that critical in my opinion, so I stopped using the extravagant set-up.