Just a small bit of grit somewhere on the mating surfaces can cause a click or a creak that drives you nuts.
I would go along with that. Also, noises sometimes appear to be coming from somewhere totally different to where they originate.
I bought a new bike last month, and after about 150 miles a 'click' developed which coincided with every revolution of the crank/chainwheel. Deeply irritating!! The bottom bracket on mine is one of those BB30's, and read various stories online etc about how easily 'clicks' can occur with them, so the BB30 was taken apart, and reinstalled. That did not cure anything, the noise was still there ....
The only other thing that coincided with every turn of the crank was the pedals, so out of desperation I fitted an old pair of worn toe-clip style pedals from a spare bike, in place of my nice new clipless ones which were on the new bike. BINGO!! The noise disappeared. So somehow the brand new clipless pedals were creating a 'click', and the bearings and such were thoroughly checked but they were fine, so finally I coated the pedal spindle threads, which screw into the crank arms, with anti-seize Copper grease. That cured the 'clicking' noise, it was no more.
Presumably the bone-dry thread on the new pedal spindles was somehow 'fretting' with the crank arm threads (particularly when under load) and somehow creating a very irritating 'click', even though the pedals were correctly tightened into the crank arms.