If you are flying a perk plane and earn ANY POINTS AT ALL, and you lose that perk plane, those perks are SUBTRACTED from your tally. They hurt you, not help you. It has been this way forever.
I have done this as well. I would take a chog (and I would click "fly" from the hangar, so I'd know exactly what the cost was), and I'd get a kill or two, and die, and back in the hangar it says I lost more than I paid for it.
Folks have also mentioned the same bug in the Tiger tanks. If you get any kills and you die, you lost that many perks that you should have just earned. They are added to the negative tally.
It's been that way a long long long time. I noticed this over a year ago, but then so did a lot of other folks, so I never mentioned it.
EDIT: Unless the perk multiplier doesn't update in real-time when looking at it in the hangar. That might explain things a bit better. Otherwise I'm inclined to think there's a math bug at fault somewhere.