Mine was exactly like yours. Yours will just need more futzing. Dont be afraid to try to adjust the fabric. For the stitch under the chin, just pull it underneath and smoothen it out with your fingers. It should almost disappear.
For the shoulders, there's a layer of clothing underneath that's there so that the Joints wont be obvious. I thought mine was broken also cause one shoulder looked smooth, then one was funky. But right out of the box, on the one with the funky shoulder, there was a lot of excess black undershirt on that arm. So I figured, by pushing that undershirt up more, it would cover the shoulders and smooth it out. Sure enough, after futzing with it, it looked just like the other shoulder. That's the reason why this figure looks bad ass, HT pretty much copied the same concept of the original Spiderman suit. Tobey wore a muscle suit underneath the regular suit, That's why he looked muscular. Hot Toys used an undershirt underneath so that it would smoothen the muscles of the truetype so it wont look toylike.
