As Loupdinour implied isn't that how the upgrade of a damaged ship has always worked?
IIRC whenever you upgrade an undamaged ship then during the upgrade it goes to 1 HP out of 1 HP max. If the ship is damaged then while its being upgraded it can have a negative HP. I've never had a ship being upgraded attacked, generally because I park a top line fleet on top of my upgrading ships, so I don't know what happens if it is attacked but I don't believe this is considered a bug.