There have been some issues with disc brakes, some of which I have only heard about, others which I have seen for myself:

1. Anecdotal: They are very strong, and so if you brake too hard with the front brake, you risk going over the handlebars. I don't know how true this is, but I think I've read it on occasion.
2. Anecdotal: The front disc brake puts a lot of tortion stress on the wheel, which tends to pull it out of the dropout, thus producing the possibility of a catastrophic crash on bikes with quick release hubs that haven't been tightened properly. I don't know if this is still an issue, since all front forks now seem to have "lawyer lips" which prevent the wheel from disengaging unless the quick release is manually loosened.
3. Anecdotal: Fork stress. The tortion causes stresses to be put on the fork, which could cause handling problems or even failure. Some bike makers (e.g. Tout Terrain) make forks specially strengthened to compensate.
4. Personal experience: Clearances can be complicated for mounting racks and kickstands. The disc brake housing tends to go just where you want to be attaching these things. For example, I cannot put a standard rear rack on my Novara Safari because of the disc brake mount position and housing; also, I cannot mount my favorite kickstand, the Greenfield.
5. Debatable: Complexity, and less availability of parts abroad, since disc brakes are relatively newer than the classic cantis.

Having said all that, there are benefits to disc brakes:

1. They are indeed very strong! Good for stopping a loaded bicycle on steep downhills.
2. Less risk of blowing out your tires on long descents because of heated up rims
3. Less wear on your rims, thus lengthening their useful life
4. If your rim goes out of true, then it doesn't affect braking
5. You could, on bikes with enough clearance, use either 700C or 26" wheels.
6. Disc brake pads tend to last a lot longer than rim brake pads
7. Better braking in the wet, and less clogging in muddy or snowy conditions

I guess there are pros and cons to any system; it depends on what is important to you and what you're willing to put up with.

Neil