It's fine as long as you can get it out. Looks like you have a bit of stopper sticking out the top which is good. On more than one occasion I've pushed the stopper in flush with the top of the opening, it's a real PITA to get out then.
It's also difficult at times to get a decent seal with a rubber stopper on a Better Bottle. The orange carboy caps are a nice replacement for stoppers.