Bombers have a minimum lead-in distance required to the target when they start their run to be able to drop their bombs correctly. If the target is too close, they overfly it and eventually circle back to try again, but at that point if there are any air defenses at all, your bombers are probably toast.

Another thing about bombers is that they make a more 'direct' run vs a target that you have a visual LOS on (using scout planes, or send a swarm of fighters to saturate the air defenses with targets and clear FoW). If you target a radar blip w/ bombers, your squadron first fans out all over the map before starting their run from multiple compass points, usually getting themselves blown to hell in the process. So you want a visual first for the best results in a successful surgical strike. (in SP, I used to do this with a single scout by pausing the game once I had established LOS and setting the target while paused. Without pausing, you just need to be faster, or use a modest swarm of fighters to get visual LOS)

Also, elevation can really mess up bomber targeting. For example, in the Arm campaign on the map that first introduces the air factory, you can't bomb enemies that are up high on a butte. Frustrating.

The T1 bombers were always more finicky in this regard. The T2 bombers are far more dependable. T2 fighters are actually excellent at ground attack as well (and surviving to tell about it).