Brute, this was supposedly fixed in patch 1.0.1. They also added a blue text in the form of a holographic light to the nodes to make them more noticeable. I have still come across this issue but it is far less common since the patch.
When obtaining these through Archeology missions the amount you receive may vary between 1 - 7. There is always the possibility for more if the mission is a 'crit.' They can also be obtained through lockboxes, though it is unknown if they are limited to a specific lockbox at this point in time.
Amorphous Crystal's are used in Artificing to create Gem's to change the color of your lightsaber/pistol shots as well as augment their statistics. They are gathered through Archaeology and are fairly common throughout most open world areas.
They are the first tier of crystal for crafting in Artificing at least.