There is a non removable, outward protruding speck on my MacBook screen, Apple is denying warranty coverage
Hard to tell without the benefit of 3D vision, but to me that looks like the screen has been punctured from the outside [the small bubbles would seem to confirm it's a puncture].
Bear in mind that anything sharp enough to penetrate through to the actual screen may leave a partially raised 'wound' on the protective layer, which you could mistake for damage coming from within. I'm pretty sure a thunderfly wouldn't be tough enough to be a cause.. they also have legs you'd see under a microscope, even if squished.