Check your reputation in your right hand screen status menu.
I've noticed this discrepancy before, the faction adjustment shown within the mission result is your underlying reputation with that minor faction. But that is superceded by your overall reputation standing with The Empire - which is shown from the status menu in the right hand screen.
I've had missions that have only shown me as friendly with the minor faction in the mission resolution panel, but because the Empire is my ally, I'm always credited as an ally for the minor faction. That applies even to Imperial minor factions that I've only just met - it's great!
The rest of the statistics make sense, what you did in your mission had some negative consequences but also increased the influence of the faction you did it for - a "you can't make an omelette without breaking eggs" scenario. It also harmed their opposition.
EDIT - Something else just occurred to me, try jumping to a different system. I had a weird bug where my faction was shown to have dropped - the mission in question had no negative connotations, I jumped to a different system and it self corrected. So it may be a display bug.