It is something we see time and again, someone comes into the studio with a bike they have gotten a great deal on in the sales and are having lots of little niggles whilst riding. Aching in the lower back and between the shoulders, knees are 'burning' whilst riding or even hands going numb. These alone are not necessarily symptomatic of the bike being the wrong size and can almost always be accounted for through fitting techniques to improve the position of the bike.
But, it may mean to obtain the position necessary on the bike a largely angled, short stem with plenty of spacers beneath it is needed to alleviate excess reach and drop to the bars. This although practical and a functional way of getting the bike to the correct position may damage the aesthetics of your lovely new bike. It may also have a slightly negative effect on the handling through flex at the front of the bike if too much steerer tube is sat outside of the head tube.
The short of the above scenario is that the bike chosen is often too race-oriented for the rider. This is definitely the most common issue we see with riders coming in to us with problems. Race-oriented bikes tend to have shorter head tubes and longer top tubes meaning that the reach from the saddle to the handlebars is a long way and that there is also a large amount of height drop between them. This is ideal when racing as it gives a 'long and low' position to reduce drag and get as much weight over the pedals as possible for power generation. However, for a long weekend club run or sportives these bikes can often feel too aggressive.
Most manufacturers now offer bikes in what they class as 'Endurance' geometry. Examples being the Argon18 Krypton, Trek Domane, Specialized Roubaix, Cannondale Synapse and Canyon Endurace amongst many others. These are all bikes that come with a slightly more comfort-based geometry as they appreciate this is necessary for longer/all day riding. This geometry usually includes a taller head tube that allow us to get a more upright position without the need for extra spacers or angled stems.