Almost all custom unit sprites are causing two graphic bugs:
1) selecting of small provinces is impossible if army is in;
2) misplacement of fighting animation in combat screen.
Now I will explain why are these bugs caused and suggest how to correct them. It would be good if unit makers correct the sprites they have already done and continue with creating sprites without these bugs.
Selecting
Each unit sprite contains several phases. Compared with vanilla sprites most of the custom sprites have large phases with unit picture in the mid.
Using large phases isn't very clever. Maybe it's only lesser work if you are converting units from Civ.
Game engine of EU select the unit whenever you click anywhere on the phase's rectangle. If the phase's rectangle is large, you will have problems with selecting small provinces.
Reduce the phase's size as much as possible.
Remember only to that, that the phase's length (size x) MUST be even number (not odd) otherwise the sprite will be flashing.
Combat misplacement
Position of the sprite on a map is controled by parameter "Origin" in SPR file. But position of sprite on the combat screen is hardcoded.
As you see, large phases with unit in the mid are sending the battle animation almost out of the combat screen. If you reduce the phase size, the units will move closer to the center of battlefield.
But sadly the reducing of phase's size in the attack sprites isn't so easy as in other (walk or stand) sprites. If you only reduce the phase's size as much as possible, something like this could happen:
To correct this you must insert "distance borders" to the phases.
Sometimes it's good to insert "distance borders" to the top of the sprite if you need to move the animation down.
Now it should work correctly. But I take it little bit further.
Unification of attack sprites
Setting the phase to fit the battlefield regardless on the other unit sprites needn't be the best way. Let unify the position of the units in the attack sprites. As reference values we could use vanilla positions.
Moving the custom unit pictures to the same position as in vanilla sprites would unify the combat sprites and make each custom unit able to fight with any other unit (custom or vanilla) without causing graphic bugs.
If the unit picture is so large that it is unable to place it in the unified position (cavalry, elephant and few infantry), move it as close to the unified position as possible.
1) selecting of small provinces is impossible if army is in;
2) misplacement of fighting animation in combat screen.
Now I will explain why are these bugs caused and suggest how to correct them. It would be good if unit makers correct the sprites they have already done and continue with creating sprites without these bugs.
Selecting
Each unit sprite contains several phases. Compared with vanilla sprites most of the custom sprites have large phases with unit picture in the mid.

Using large phases isn't very clever. Maybe it's only lesser work if you are converting units from Civ.
Game engine of EU select the unit whenever you click anywhere on the phase's rectangle. If the phase's rectangle is large, you will have problems with selecting small provinces.

Reduce the phase's size as much as possible.
Remember only to that, that the phase's length (size x) MUST be even number (not odd) otherwise the sprite will be flashing.
Combat misplacement
Position of the sprite on a map is controled by parameter "Origin" in SPR file. But position of sprite on the combat screen is hardcoded.

As you see, large phases with unit in the mid are sending the battle animation almost out of the combat screen. If you reduce the phase size, the units will move closer to the center of battlefield.
But sadly the reducing of phase's size in the attack sprites isn't so easy as in other (walk or stand) sprites. If you only reduce the phase's size as much as possible, something like this could happen:

To correct this you must insert "distance borders" to the phases.

Sometimes it's good to insert "distance borders" to the top of the sprite if you need to move the animation down.

Now it should work correctly. But I take it little bit further.
Unification of attack sprites
Setting the phase to fit the battlefield regardless on the other unit sprites needn't be the best way. Let unify the position of the units in the attack sprites. As reference values we could use vanilla positions.

Moving the custom unit pictures to the same position as in vanilla sprites would unify the combat sprites and make each custom unit able to fight with any other unit (custom or vanilla) without causing graphic bugs.
If the unit picture is so large that it is unable to place it in the unified position (cavalry, elephant and few infantry), move it as close to the unified position as possible.