I have a one year research project in my MSc curriculum. So i was suppose to address a existing issue in bitcoin protocol. Highly appreciate if someone can advise me and give me some ideas.
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Selfish mining is probably one of the most addressed issues that was theorized by a group at Cornell university. I find this interesting, because rather than being a technical issue such as transaction malleability, it is more of a conceptual issue with how Bitcoin and its consensus system works.
That should get you started and give you some food for thought.