This is why I can't combo for extended periods when leveling all night. I've had tendonitis in the past and have been tested for carpal tunnel syndrome because the pain has been so bad before. Now, when I start to hurt like that, I just take a break. It's quite possible to injure yourself doing this if you ignore the pain, so never take a painkiller and keep playing, that will only make it worse in the long run.
Btw, zero's musician exercises sound like a good idea.