I used to have a problem with trypophobia, but not anymore, and I'm pretty sure I know why. I was also terrified by close-up pictures of spider faces without exactly being afraid of spiders themselves because of how their eyes appear. Their eyes, in a way, look like a cluster of holes. There's an order to them, like the fact their usually structures into bands like the anterior row of eyes, a dorsal row, etc. but they still look like a cluster of holes.
Well anyway, through a process I got over that fear of spider eyes and I guess the trypophobia came along with it.
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Essy, Avian Enthusiast