A few reasons for a bike fit 1 to 7.
A lot of people put up with below because I think 'well it's a bike so there must be some discomfort'. Riders put up with bad because they have never experienced what good feels like.
There is lot more issues than this, but this is some of my observations and opinions on some of the things people have problems with and just put up with.
1. Hand pain/numbness - too much weight on the bars, causing you to lock your arms out due to supporting a lot of your body weight, normally due to one or all of these, saddle too far forward, nose pointing down especially if nose is lower than the middle of the saddle and/or saddle too high causing you to ride on the nose of the saddle as your body tries to maintain a shorter leg extension. Also if the angle of handlebars and brake levers are setup wrong this can cause the same issues, if levers are to far forward this will cause you to over reach and cause you to over extend your arms, again putting your weight on your bars.
2. Shoulder pain - due to all of the above, i e supporting most of your body weight on your shoulders with arms locked out.
3. Neck pain - due to the above if you are to far forward you have to pull your head back more, causing you to fight locked out arms and shoulders.
4. Tried 'dozens' of saddles - saddle discomfort often has nothing to do with the saddle, as well as the above if the angle of the handlebars is wrong this can cause your pelvis to tilt forward putting pressure on the pubic area. I had one person who came for a fit who had bought a dozen saddles, not from me by the way as I wouldn't of let them buy/try that many, as I know there is more to a saddle than how it looks or feels with your fingers, in the end I fitted him to the second saddle he had bought, but because the angle of his drops and hoods were wrong no saddle was going to feel good, but once I'd adjusted bars and levers that saddle felt great. I can change the way a good saddle feels just by changing the angle of bars and break levers, but most people would blame saddle discomfort on the saddle not on the handlebars.
5. Can't ride on the drops - a lot to do with above 1, 2 and 3. People think it is a lot to do with flexibility, height and reach of bars and stem, but if the angle of the drops points down towards the back wheel even with good flexibility you will struggle. Compact bars are by the best to fit.
6. Bike handles badly - too much weight on the front wheel due a lot to 1, 2 and 3. Riders will blame the bike, but you can be the biggest influence on how a bike handles for good and bad, geometry between a similar size frames across brands is not that different, the way the contact points are set up, i e saddle height/layback/angle, handlebar/lever height/reach/angle can have more of an influence on handling. You might read a great review about a bike that has been perfectly set up by the tester, but if you get the same bike and it's not properly set up to you it may handle like a bag of 'spanners', and you'll think what was the reviewer on about.
7. Trouble feeding on the bike - this is something people don't think about when it comes to a good fit, they think it's about pedalling performance, but if you can't feed your pedalling performance will be reduced. Again back to 1, 2, 3 as well as 6, due to you having too much weight on the front you are unable to flex your elbows allowing them to rise and fall freely, if you can't do that most people are fearful of taking their hands of the bars because the bike feels so twitchy. I've had the some people that before being fitted they have had to stop to feed because the bike handles so badly.