The bomb explodes at the top center point of the square tile regardless of where in the tile you aim (in places where you can see the tile, like Oryx 1, it is easy to see this) if you are near 0 degrees rotation. At angles nearer to 45 degrees, it explodes at the topmost corner of the tile.
The old rule-of-thumb is to aim at the feet of the enemies (practicing on constructs helped me a lot). Also, say in case of a crystal, you can try rotating around until finding the point that can pop on the crystal…
Edit: Also, I’m not sure the hitbox size of all enemies, but assuming there are some smaller than the size of a tile, it could be the case that it is impossible to hit the perfect spellbomb if the enemy hitbox isn’t on the top-center or top-corner of a tile.
Edit 2: And as others have stated, it is highly affected by lag. Sometimes an enemy can only register so many bullets at once, and so if spellbombing a crowded drop-chest for example, you can notice most shots missing and sometimes hitting the perfect spell bomb. These seems mostly affected by how many people are shooting the enemy, but it can happen with just one spellbomb shot as well.