Look at these two diagrams:
Picture your macro lens -- probably it's maximum aperture (f/stop) is f2.8. That's as large as the lens opening can go. Its minimum aperture is f22 or f32; its smallest opening. Notice that when you shoot "wide open" you get very little depth-of-field, an effect even more pronounced with a macro lens. Depth-of-field increases as the size of the lens opening (actually its diaphram) decreases. Let's look at these samples:
Taken at widest opening, f/2.8 with my 100mm Macro
Taken at f8
Taken at f/32
In each case I was focusing on the very same spot, the 6th shade tab. There is practically no depth-of-field at f2.8, so although the tab I focused on is sharp as a tack, the image overall looks out of focus. At f8 we see a good deal more sharpness, but still a lot of fall-off at the extreme front and back. But at f32, the image overall looks acceptably sharp.
When I teach my workshops, I recommend that every shot be made at f32. We let our TTL flash do all the work of giving us correct exposure each time, and so we can be confident that all of our intraoral imaging will look nice and sharp. It's also a lot easier, and less error-prone, than fiddling around changing our lens setting with each shot!
Make sense? Drop me note. A sharp one, please!