One is when you are close to a station. you simply cannot target the station unless you are over about 5 clicks away when you need to be closer than that to get docking permission. So you have to go to map and manually click the station and press T to target it so you can dock, far too often.
The other is when you are opposite a component on the surface of a ship you are fighting, when you can line up the crosshairs on a component, activate target under crosshairs and the game will select anything but the thing you are trying to target, especially if there is something on the other side of the vessel which intersects with the hitbox.
So you have to...
- stop the game and try to select it with your mouse or
- select nearest enemy, cycle through the many components to get to the one you want or
- select nearest enemy, press external view twice, then navigate around the object and select a component using the mouse, when the engine plumes or the ship's own selection box can obstruct selecting components.