Copyright issue
Since originally, Notch has not licensed Minicraft under any license explicitly.[1] With just the declaration, it cannot be said that derivatives are completely legal. In addition, Notch stated that he cannot be sure whether Minicraft is included in sale to Microsoft.[2] Therefore, the copyright owner of Minicraft can be either Notch or Microsoft, so even Notch agreed, Microsoft still has the ability to sue the developers, unless the state of copyright is further confirmed by Notch.
Minicraft+
This also affects client instances of Minicraft+. Even if the amount of code updates is enough to say the codebase cannot be affected by the state of license to the original game[3], the assets (audio and textures) are still the original ones. Unless the assets are further reworked, this could allow the copyright owner to sue the Minicraft+ development team, once they would like to. This can break the state of being "open source" for the project.
After further discussion by the Minicraft+ team, the conclusion stated that it is possible that if Microsoft is the copyright owner, they would first try to purchase the project when the project is enough popular.[3] However, the validity of this conclusion might be under uncertainty due to the unpopularity of the game. At the moment, this issue might be ignored as of the practice that big company would not take legal actions to small projects.