If coming from a lower resolution camera to the 15MP 50D, when you are viewing the images at 100%, you are looking at them enlarged a whole lot more than you might be accustomed to doing with earlier, lower resolution cameras. Using 50D, 7D and 5D MkII, I seldom evaluate focus at more than 50% (I'll zoom in further to do fine retouching, if necessary).
Also, pretty much all digital images need some sharpening to bring out the fine details. The higher the camera's resolution, the more sharpening is usually needed.
And, the more resolution a camera produces, the greater the chances it will out-resolve some lenses. This includes that the greater the resolution, the more you will see lens flaws such as color fringing (chromatic aberration). Zoom in far enough with even the best lens and camera and you can find some "issues", but zoom back out to more realistic sizes and they disappear.
There are several things you can do to maximize your focus accuracy....
1. Remove "protection" filters. The higher quality ones will have little effect unless strong stray light strikes them directly. Low quality ones can cause all kinds of focus problems, even cause color fringing (chromatic aberrations) and image softness.
2. Use a lens hood. By shading the lens the AF system will work faster and more precisely.
3. With most Canon, select the center AF point, it's the most sensitive.
4. With most Canon, use One Shot with static subjects, it's more precise than AI Servo.
5. Manual focus using the AF confirmation (beep and green LED) along with some sort of focus magnifier, such as the Angle Finder. There are alternative focus screens available for the 50D, some of which might help with manual focus accuracy.
6. Use Custom Function III - 7 and Micro Adjust the focus of each of your lenses (up to 20). See the manual for detailed instructions. This is most effective with prime lenses. A zoom necessarily has to be adjusted to a compromise or average, at two or more of it's various focal lengths.
7. Before you get too critical with the camera or your lenses, and when testing, evaluating and adjusting them, consider your computer monitor. Most consumer grade monitors cannot display all the detail in an image. Print images out on a high quality, smooth matte paper for the most critical evaluation of image sharpness and precision. Depending upon the quality of your printer, it can be surprising how much more detail and sharpness an image might have.
8. All lenses have a "sweet spot" aperture where they are at their sharpest. Usually this is a middle aperture such as f5.6 or f8. But some lenses are designed to be very sharp wide open (ex.: 300/2.8 IS) or stopped down a lot (most macro lenses).
9. With digital sensors the size of the one in the 50D, at it's level of resolution, the camera's optimal aperture is most likely around f7. Smaller apertures will gradually show increased loss due to diffraction.
10. DSLRs using crop sensors, like the 50D, have somewhat restricted viewfinders that make it hard to evaluate focus and depth of field precisely. Autofocus camera's have largely done away with some of the focus aids we used to enjoy with manual focus lenses. Stop down an extra stop, for highly precise work you might want to use a hyperfocal distance chart.
11. Watch out for slow shutter speeds. Camera shake can look like missed/inaccurate focus. Best to use a tripod for focus tests and micro adjusting.
12. Image Stabilization can also cause "shake" in images, if used incorrectly. Shooting too fast with IS is one common thing. It takes a fraction of a second to stabilize effectively. If you put some IS lenses on a tripod, solidly locked down, you need to turn it off, or it can cause image blurring.
Some lenses are simply sharper than others. I use 300/2.8 a lot, but it's mostly a tripod lens. So I also use 300/4 quite a bit, handheld. If I look closely I can see the difference, the f2.8 lens is simply sharper and delivers more fine detail.
I was working on an 11x14 image, printing it out to be framed. All the while that I was zoomed way in and doing some fine retouching and adjustments, I thought I'd shot it with my 5D MkII. But when I happened to look at the EXIF data, I was pleasantly surprised to see it was actually shot with one of my 50Ds (and an EF 20/2.8 lens that was fitted with a B+W Kaeseman Circular Polarizer at the time). The print from my HP B9180 is even better than what I can see on my computer monitor. Not every image coming out of 50D is that good. I just managed to hit the sweet spot of everything with that particular image. I wish I could do that every time. I can't.
Shooting action, with 50D I see about 5% of images where the AF misses or loses the subject I'm tracking. It happens. Can't be helped and I think 95% "acceptably in focus" is pretty darned good.