Then we should see a very bright border as matter and anti-matter annihilate on the edges. As far as I know, that doesn't exist so being a bubble of matter in anti-matter doesn't seem likely.
We have no idea what portion of the universe is observable to us. It could be a small fraction, or a large fraction, or even more than 100% (we could be seeing parts from different directions). If we can only observe a small fraction, then it's possible that the universe is half matter and half anti-matter, with the boundary beyond our ability to see.
However, science only deals with what we can observe, so there's not much point in worrying about the possibility. We also assume that there's nothing particularly special about our art of the universe as compared to the rest. That's served us pretty well, but it could be overturned by observation -- for example, our location within the galaxy is actually a bit atypical.