Curious... and I ask this because I know if I were the service manager, it would be my first line of thought... what type of work were they performing on your car? Was it anything where they should have been anywhere near the intercooler in the first place? I mean, if you were to have your rear brakes replaced, as the service manager, I would wonder whether my guys had actually been responsible for bending intercooler fins. But if they were doing a tune-up & replacing spark plugs, which requires IC removal, I could see them inadvertently bending some fins.
I ask this to gauge the service manager's point of view, basically. If they were working in & around the IC, then he's got to at least admit that they could have inadvertently screwed some up. If they weren't under the hood, I would expect him to be a bit less receptive to your claim.
In the end, though, it's going to come down to this- there's no way for you to prove that the IC was unblemished when the car went in. It's your word against his tech. (Unless the tech admits to goofing, of course.) The determining factor is going to be his dealership's desire to retain you as a customer. If they are a service-oriented dealership, they would likely either eat the cost of a replacement IC or at least give you a deep discount.
But in this day & economic climate, I'm going to bet they go with the "no way to prove it happened here" spiel, and you're going to be on your own. I hope I'm wrong, though.