Anytime a deer is gut shot it usually takes a considerable amount of time for it to expire. It is most likely that the deer did not cool down enough on the inside to prevent gas formation. Being gut shot the stomach juices were most likely released inside the cavity and would be absorded into the surrounding meat.
You most likely noticed a strong odor when field dressing the deer, it's my guess that this odor is what made your processor feel that it was no good.
As to the internal bleeding that in my opinion has little or nothing to do with it.
    The problem is being gut shot and the time it took to find the deer. As far as edibility, yes it most likely was edible. As far as palatability it would not be the best if there was a significant amount of bloating.
    If it was rinsed throughly, liberally sprinkled with baking soda in the cavity, allowed to hang awhile and then rinsed again it could have helped the situation.
    Next time someone else processes for you I would ask them to call you before discarding the deer so you can make the judgment call.

Dave