I had the same problem. I had bought used , fungus infected Yashica 50mm ML F2.0 lens from
eBay. Thoroughly cleaned it and encountered this issue on the first roll itself. Since I was using an old self serviced Yashica Fx3 camera, the suspicion first went to camera and then to the lens. I do not know how much time I spent in trying to set the lens so that it did not protrude out on the back side of the lens when focused to infinity. When it did not succeed, I started looking out for others facing the same problems and voila, I find this life saving forum. I indeed had the same problem of mirror protruding out. Used hair drier for heating the back side of the mirror while in B mode and pushed it back slowly in 2-3 iterations. Fixed the issue and now all seems to working great. Thanks guys.