Why in some cells is GTP made in citric acid cycle and in some ATP?
This step is catalyzed by succinyl-CoA synthase which has two different isoforms- one which produces GTP while the other produced ATP.
It seems from this study that predominantly anabolic tissues prefer the GTP-producing form whereas the predominantly catabolic tissues use the ATP-producing from. 
In the same paper they discuss that GTP is important for protein synthesis and it is also involved in production of phospho-enolpyruvate by PEP-carboxykinase in mitochondria; therefore playing an important role in anabolic processes.