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That intuition is correct. Hardware isn't a magical exactly perfect thing every time. Everything has "flaws" and so you set tolerance levels and do your best.
CPUs and GPUs and RAM and drives all have specs they are aiming for, like a CPU manufacturer may want the next chips on the assembly line to be >4ghz, they crank out 1,000 of them and benchmark them. Some hit 4, some do 3.9, some may be 4.1 even. As long as it's above spec it gets labeled the 4ghz Ultra or whatever brand. But the chips that run fine, but are slower, say 3.5ghz, then they just slap the 3.5ghz Mideange Label on those and sell for %20 less. The ones coming out at 3ghz get the Low End Label and are half the price.
That way they sell them all and everyone is happy (mostly).
Also that pesky law of thermodynamics ruins our fun and hardware gets worse over time too. Depends on the defects and lots of variables, but maybe one case didn't cool as well so the CPU gets hotter and it had a defect that degraded it's speed a bit so now that 4ghz Ultra is actually running at 3ghz, but that happened after the user bought it, so it is just "a slow machine" as you said.
It's very real and you aren't crazy for feeling like or even proving that some really are slower than others.