After a good night's rest, you should wake up feeling your best physically because everyone's body has a self-healing mechanism and that takes place when sound asleep.
Morning aches and pain are a sign that something that happened yesterday and/or through the night did not go quite according to plan to allow the body to fully heal.
This can happen in all parts of the body be it a healing fracture, ligament or muscle strain.
Generically speaking, there are 3 possible categories where your reasons might fall into:
1) Poor sleeping posture causing discomfort in your joint as you prolong that position e.g. sleeping on an injured shoulder; hotel mattresses that are too soft for your back; using a pillow too low/high.
2) Accumulated inflammation from the day before through the activities you brought that joint through. A minor injury in the day should not generate so much inflammation that your body is unable to deal with through a good 5-6 hrs of sleep.
3) Lack of quality rest. Keeping to rest days and maintaining sleep hygiene is paramount to recovery along with good nutrition and mood management. Without giving your body enough time to heal, residual injury accumulates through time and gradually presents as pain when your body's tolerance is exceeded. This can take between a week to months or years depending on your lifestyle.
Take home message:
Don't ignore the early warning signs from your body!
If you're not able to recover naturally, there definitely is something detrimental going on with what you put your body through.
Better seek professional help sooner than later!