1 Seems that is the maximum angle admissible with the inclined lateral planar face and the top arc-circle 0.99....
If the lateral face was not inclined but perpendicular sure you should go to the same 0.99...

2 Maybe you have made a "Trim" action and not a boolean difference so the volume was stay "open"
and now some actions will be necessary for close it :)

3 when you make a fillet to a whole piece, general fillet is adapted to the less acceptable minimum angle somewhere!