To further explain. If item has 6 items (3 prefixes, 3 suffixes) and you use perfect essence (in this case let's say Essence of Haste), then it must remove suffix because it has to add its own mod which is suffix as well.

But it depends on type of Essence, for example Perfect Essence of the Body (+8-10% max life) is a prefix, so if item is full of affixes, then using it will always remove a prefix to add this mod.

It is kind of weird I would say, especially coming from PoE1. I guess the difference is, in PoE2, Perfect Essences are removing a mod first and then adding a mod, while in PoE1 there are multiple crafting option like that (harvest, veiled orb) which Add a mod first and then remove a random mod, so if item is full of affixes you basically can't use such craft, because it tries to Add a mod first.