I have experienced a similar discomfort in the last 2 weeks. The way I overcame this problem was to really squeeze my traps together under the bar and take a slightly narrower grip on the bar beside my shoulders, this helps maintain the flexed traps. I then try not to bend my wrists back under the bar but instead keep them straight and try to lock the bar on the fleshiest part of my traps which once flexed creates a shelf so to speak. Also when you go under the bar, get your mind into an attack it kind of mode (kinda get pissed off at it a bit for intensity), this helps blood flow into the traps (advice I got off a heavy lifter in my gym). This all helps to provide a good cushion that is much harder thus stopping the bar tearing and bruising the back up. Other than that, you could take the advice my gym partner gave me; "take a concrete pill and harden the F@#K UP", LOL.
Make sure you lock the bar, its the slight movement that creates the blood spots and bruising on the back.