It kind of sounds like what happened to me when I got bucked at. It was bruised and after a few days a lump formed, like proud tissue. Its hard to explain... It was like the kick had ripped a muscle of something tissuey under the skin and as it healed a scab formed under the skin...
It could be similar for your horse... Got kicked, bruised but no broken skin and there is proud tissue where a muscle was damaged and now is repairing. It took ages for my lump to dissapear but it did!
Just a guess. Think it may be possible?
~I live for the moment when a creature with a spirit wild and heart untouched puts its head in your arms and falls asleep~