There is a non removable, outward protruding speck on my MacBook screen, Apple is denying warranty coverage
Solution 1:
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.