I think my Armorer ran into this same problem last night. There she is, hammering away at the forge when an event pops up. She takes the appropriate action to counter the event, the icon goes green and the sucessfully countered the event message pops up, but the numbers overhead are -55 + 40. It seemed to happen on about half the events that used the firey red icon. It didn't stop her from finishing her level 50 rush orders at 51 with time to spare, but it's pretty annoying, especially when I seem to get critical sucesses about 25% of the time when I'm NOT paying attention and don't properly counter things with my Tailor. To try and work around it I started using durability counters when that event icon popped up if I was close to the finish and I don't recall getting a negative number that way