Even though germs are very small they usually have complex structures which can get damaged by soap and disinfectants this killing them most smell come from much tinier lipid particles. For example one component of the smell of feces is skatole a tiny organic compound. This can be harder to wash off.
The outer surface of your skin is covered in many layers of overlapping dead skin cells. Unless you have a skin infection, bacteria don’t make it past the first few easily-washed-off flakes, and your immune system destroys them if they do.
Smelly molecules like fish or skunk are much smaller than bacteria, so they can penetrate much deeper into your skin; also, your deeper skin layers don’t actively clear them away like they do bacteria. To get rid of them once they’ve soaked in, you’d have to scrub your skin raw, or just wait for them to slowly diffuse away on their own.
Germs are thousands of times bigger than smells.
For a real ELI5: If you spill marbles on the floor, you can “wipe” them into a pile. If you spill flour, there’s almost always a trace left behind unless you work very hard. Because the flour particles are so much smaller than what you’re wiping with.
Skin isn’t smooth and try to think about it like it was a carpet. Germs and bacteria are bigger than smell particles.
Drop some relatively big on the carpet, like a coin, and it’s really easy to pick up, leaving no evidence that there was a coin on your carpet. But then spill sand on it or something powdery, and it would take a really long time to really clean that carpet.
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