It has been said that bumblebees should not be able to fly, based on their body mass and their wings. This is, of course, untrue: bumblebees follow natural laws and their flight makes sense from a naturalistic perspective.
However, let us say that we studied bees up and down, backwards and forwards, in wind tunnels, with high motion cameras, in every possible way and determined that in fact, they can't fly. No naturalistic explanation is available, no naturalistic explanation is possible. In fact, we discover that if you clip a bumblebees wings, as long as you leave enough wing to move any air whatsoever, the bumblebee flies as if the wing weren't damaged at all.
Such a finding, if sufficiently rigorous, would definitely put a serious dent in naturalism... especially if bumblebees were the only insect about which this were true.
The reason these would be tough is because in the case of the bumblebee, we have close anatomical relatives (like the carpenter bee) that have flight that makes sense. Everything else, everywhere, would be seen to observe the fundamental laws of physics but for some unknown, and possibly unknowable reason, Bumblebees would not. Not because we don't understand flight, but because even when we do things that absolutely should affect their flight it just doesn't. They would be an exception, and far from proving the rule, exceptions to your rules mean your rules are incomplete.