I have a thesis due in two weeks so I haven't had time to write much.
I would like to answer Edward who wrote that joint damage is unavoidable in Aikido.
Here's why I think it's complicated:
1. Flexibility can be good or bad. If a joint is too flexible, it can move beyond the range that's anatomically supposed to move in and that could cause it to be put in a 'weak' position while you're asking it to bear a lot of weight (kind of like being off-center except for your joints)
2. If you have uneven muscle development or tension your own body could be pulling your should out of place as you use it again leading to a weak position, grinding, swelling, etc...
3. If it hurts when you move it or it grinds when you move it (even a little) ... and sometimes even if it pops when you move it... it means you're irritating something which is going to swell, leading to grindings, more swelling, etc...
For some answers:
1. I'd like to second Colleen. Another explanation: if you let it rest, the swelling will go away, if the swelling goes away, exercise is less likely to irritate the joint, then you can return to training
2. You might need to warm up more than your fellow students.... When you warm up (properly) you add more lubrication to a joint which can let even a damaged joint work without more irritation.
3. Stretch to get your muscles (you shouldn't stretch ligaments or tendons much) warm and ready for class, don't do it to see how far you can stretch.
4. Be aware of how your joints move (this takes about as much practice as Aikido, but a little can go a long way) There's a natural way and there's everything else.
leaving your shoulder blades in a neutral position and your arms straight, see what the range of motion is for your shoulder joint. It's not really a circle, it's more circular in the front and bumpy in the back.
5. As an extension of number 4, there are worked out systems of learning about natural movement of the human body which can do amazing things for you. They have teachers and give lessons and everything... they're not an option for everybody since it takes a lot of insight and can be expensive.
I wrote this pretty fast so forgive me if I offend anyone. If you're curious about any of this I'd be happy to write more.