I own a 40D and an EF 50mm f/1.8 II lens. Can't say I ever experienced what you mention, specially when using the extra sensitive center-point. As long as the selected AF point is on the target, it usually focus accurately.
The only situation where that happens, in my experience, is when using all of the AF points, because it always focus on the closest subject. I find it mostly useless, so it's normally set in the center point. When shooting static stuff at close range using big apertures, I do select the closest AF point, since locking focus and recomposing can change the point of focus.
Other than that, maybe the bird is too small and doesn't "fill" the center-point, thus confusing the AF?