#1 Ghost Fragment: The Ocean of Storms 2
This can be found in the Circle of Bones area, found within the Hellmouth (just before you reach the summoning pits area in the Phogoth Strike). It can be found on top of the right most set of lights hanging from the ceiling as soon as you enter.
#2 Vision 47
This can be found in the Hall of Wisdom area. To get here, from the spawning zone head up the hill and then through the dome shaped building. Head down and into the hive caves. Descend the area and you will reach the hall of wisdom. Head through a little bit and then turn left (towards the Shrine of Oryx). The dead ghost can be found way up top behind some tubes. You need to jump on the tiny little thing pointing out of one of the pillars to be able to jump that high.
#3 Ghost Fragment: The Exo Stranger 2
This ghost can be found in the Summoning Pits. This area is not accessible in patrol, or any story missions (so far). You will need to enter the strike called "The Summoning Pits". Fight to the very end where you battle Phogoth. The ghost is on the beam way up in the middle of the room. To get to it, you can climb the rocks over on the left when entering, or climb the structure on the right when entering. In my opinion, it is easier to go on the right (as shown in the video). Once up on the beam, the ghost can be found on one of the supports sticking out, the one furthest left from where you enter the room.
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Credits: Special thanks to HarryNinetyFour for the video guides.