To stay in line with the original idea of this thread, here's a couple to think about:
What if a black hole isn't an object, but instead it's a entry way to another dimension or universe? It would explain about everything we observe.
If the moon causes the tides, would an increase of global sea levels slow down the earth's rotation?
Cocaine comes from coca plants, and cartels are some of the biggest businesses worldwide, why isn't anyone doing suspended cell cultures to produce it on a huge industrial scale?
All researchers who mapped the genes related to this have magically disappeared and so did most of their scientific work.
How can one prove that we're not in a matrix-like simulation? How can one disprove it?
If the weight of our microbial community outweighs our brain and has a higher metabolism, AND has been proven to affect our mood, taste, desires and mental state, how in control are we?
If an AI system would become sentient and reach the internet, wouldn't it be wise for it to lay dormant? How would we know?
When we finally produce a plastic eating bacterium or fungus, how on earth are we going to protect our food packaging from expiring before our food does?
Here's a nice conspiracy one: Let's say you're a multibillionaire, and you own enough land to keep your family safe for decades. You're completely aware that the most dangerous thing in the world is overpopulation, you've made this a spear point in almost every discussion about it. You're reaching the end of your life, you know that the current law system prevents everyone from prosecuting your family for the things you have done, but then again, they have enough money to last a couple lifetimes
and hire a private army. Would you sacrifice 10% of your one-time annual income and your good name, and possibly your life, to save the world? Why wouldn't Gates? In all honesty, he could. What's stopping Bezos? Or Gates?
If there's a genie in a bottle, granting you one wish, is there a better flaw in the system than wishing "I want everything that I write in this book to come true"?
Is the baltic sea anomaly a real thing, or a hoax?
https://en.wikipedia.org/wiki/Baltic_Sea_anomaly
Is it ethical or morally just to clone and re-introduce extinct species like the Woolly mammoth?
Plant diseases spread through the air and spread through aphids and other flying insects, do bonsai artists ever quarantine their trees after a show?