This is a delicate topic.
Before I get into the 'fleeing' part, let me bring up a similar issue I have seen players grumble over: use of healing potions.
Since we're tying in the idea of villains acting intelligently, why would they not use every item at their disposal to fight, win, survive, etc? I recall being a player in a game where the GM had a bad guy drink a healing potion and one player went nuts. It was surreal. My own was response was kind of a growl but it was because it made it tougher on us. I had no real problems with the villain doing it because it seemed intelligent and it showed the GM was clearly giving us a challenging issue. But the player who went nuts, slammed his fists, yelled and just acted like a true ass. I mean, the guy was shaking in anger.
My own experience as the GM involves supers games. I run supers more than anything else and I feel it is a common theme for villains in comics to slip away. That is kind of a thing they do. Further, ones that have illusion powers use them to their advantage and so on. A few weeks ago a team of villains really were quite bright and kept their powerful illusionist in hiding. Once things went poorly for the villains, the illusionist used her illusion abilities to create an illusion of police showing up to arrest the bad guys, allowing them to slip away with a phantom escort. I gave chances to detect the illusion, showed some strange actions with the police, etc. Some of these players got really angry at the end of the session and stormed out, leaving a bad taste in my mouth for a few weeks.
Half the players thought it was clever and the other half thought I was playing dirty pool. We never really had a discussion to resolve it but things calmed down. But based upon that, I am sure hesitant to try anything like that again due to backlash, which is unfortunate since I felt it was within their scheming, a reasonable tactic and one which was 'fair' as they got several chances to detect it. (Added was the fact that a week or two later the characters would get another shot at them as the final arc of the story involved the characters tracking them down.)
I guess what really bothered me was the fact that we have been gaming together a long time, and I have always shown a propensity for fairness and equality. The accusations of unfairness by a few of them really bothered me and left me upset for about a week over the whole thing.
So to bring it full circle, I can certainly understand why the green dragon slipped away and feel your pain for having players who felt you 'stole their kill.'