The stock setup on Rugers is pretty sorry regarding extracting/ejecting empties. You probably have the correct base pin, they are longer than Colts or older Rugers so that the base pin can't come completely out of the gun when it's out to remove the cylinder. There's a couple things you can do. Some aftermarket base pins may be available that are shorter up front. A Colt style base pin would be good, tho Colt and Ruger base pins aren't interchangable.
There's a couple other things you can do. One is technique, the other is change the extractor rod. The aftermarket rods I've used (Colt copy replacements) seemed to be a little bit longer than the factory Ruger rods. When installing them, they are actually a bit too long. I file them shorter til they stick out into the cylinder window a small amount, but wont interfer with removing the cylinder. One more part to help get cases clear. I put a Colt type extractor rod with bullseye end on it. The stock Ruger extractor rod heads are tiny. The bullseye or crescent type are a big improvement, and a cam cut extractor rod housing is also an improvement, as it allows the head to cam away from the barrel while using it, and cam back close when its at rest. Both parts are availble from one or two aftermarket parts makers.
I've shortened the factory base pins and reshaped them on all my Rugers (I detest the factory style base pin heads). Here's a pic of one I did. When shortening them, the extractor rod spring will stack up solid and needs to be shortened about 6 or 7 coils, then stretched again. It also seems to help when first assembling the stretched spring to compress it and let the rod snap back to rest several times, it never seems to have any troubles after that, otherwise its sticky at first. After doing these things, my rod comes about 3/16" past the rear of the frame at its maximum extension. This helps clear cases completely out of the gun when using the rod. The other part of the answer is technique. There are likely other ways, but I put the butt into my solar plexus, hold the gun and rotate the cylinder with my left hand, and punch the rod with my right hand. Yes,
punch the rod. I slam it hard. The cases go out under the left arm end up on the ground at about 8 o'clock (behind and beside me on my left) about 3 or 4 feet behind me when done. It takes 2 or 3 seconds to completely empty the gun this way.
Watching many shooters struggling with single actions, fiddling with each case, shaking the gun, and other slow frustrating techniques, I don't doubt that they find they dislike SA's, and think they are terrifically low to operate. Yes, they're a bit slower than DA's, but it doesnt have to be quite that bad.