Yes, and the idea, rather the fact, is that you have a problem. Because of the way the flange was rotated, the wax ring on that side is not going to seal to the bowl next to its "throat" but rather outside the anchor bolt. For this reason, you have to use two wax rings and splice them together using a piece from the second one to make the first one larger. But that will only seal the bottom of the bowl to the flange, it will not seal the "opening" where the anchor bolt is and nothing will make it waterproof. The best you can do is to fill the bolt hole with some of the left over wax from the second ring to try to make it odor proof.