I am also guilty of sewing over pins. But not any more. This weekend I hit one and it caught up with the needle and yanked the needle right out. I was very fortunate that nothing was damaged and was able to get the needle out and replace it. I think maybe the thumb screw had loosened up a bit as well. I once took a class where the instructor told a story of sewing over a pin and hit it and it shattered the needle and shards of metal flew up into her face and hit her glasses. She said if she wasn't wearing glasses it would have been ugly as the shard of needle would have gone into her eye.
But I digress, I too have seam allowance fabric sometimes bunch up or go through and end up being sewn down in the opposite direction of what I pressed it. I don't worry about it. In the end all things line up and once quilted no one will know if your seam allowance is going the wrong way.