This is a matter of debate, the Anemospilia findings have been controversial since the site was first excavated in 1979, and the Kydonia findings are quite recent; the sceleton was discovered in 2010. Insofar there has been no conclusive study of the Kydonia findings, the excavations are on going and Maria Andreadaki-Vlazaki, the archaeologist responsible and General Director of Antiquities, has mentioned that it's still too early to tell.
Peter Warren first suggested human sacrifice as a possible interpretation for the skull fragments that he discovered in 1967 in the Early Minoan settlement in Fournou Korifi:
Just beside P574, to the south-west, lay the strangest find from the site, fragments (about a quarter in all) of a human skull. Like the pots the bone was burnt by the destruction fire, but the pieces were identifiable as those of a young adult male... No other bones, human or animal, were found. How is this skull to be interpreted? It was certainly not the remains of a burial, nor could it be a last inhabitant who had failed to escape at the moment of destruction; in both cases other bones would have survived. The skull can only have been an object as such, deliberately situated near the tripartite structure with central hearth. Thus the possibilities of ancestor worship or even human sacrifice cannot be ruled out.
Source: Peter Warren, 1972, Myrtos: an early Bronze Age settlement in Crete
The discovery of the bones of four children in a Late Minoan house near the palace centre of Knossos reinforced Warren's belief that the Minoans practiced human sacrifice. Both Warren and Nikolaos Platon supported the human sacrifice interpretation, while other scholars argued that the finds suggested a secondary burial. The more sensational interpretations included cannibalism:
Matters are even more complicated with the remains of four bodies that were found in Anemospilia. The building's design is unusually symmetrical and its function can't be deduced with certainty, although most authors call it a temple. Part of the uncertainty comes from the fact that it was partially destroyed by an earthquake and/or a fire in the 17th century BC and part from its unique - for the era - design. To make matters worst, Yannis Sakellarakis, who first excavated the area in 1979, didn't publish a report of his excavation.
Sakellarakis theorized that the one body, a young adult male, was the victim of human sacrifice and the other three bodies were the priests that were conducting the ritual, killed by the earthquake, in what could only be described as an extremely bizarre occurence of events. The young adult male was found on top of what appears to be an altar, with a knife resting on top of him, and Sakellarakis believed that the ritual was a panicked attempt to satisfy the gods as the seismic activity was getting stronger. The following is a picture of the remains of the alleged victim as it was found:
Dennis Hughes is particularly doubtful of the claims made by Sakellarakis. In Human Sacrifice in Ancient Greece, he argues that the knife found on top of the body is actually a spearhead and that it could have easily dropped on top of the body from, for example, a shelf during the earthquake (pages 16-17). He is less critical of Warren's interpretations, and even presents some arguments in favour of Warren's interpretation for the childrens' bones found in Knossos (page 22).
Which brings us to Kydonia. The remains are 12 bones belonging to the same young - possibly adult - woman and were found in the courtyard of the palace, surrounded by animal bones. In the following picture the human remains are visible to the right and the horns of a Cretan Ibex are visible to the left:
Initial dating puts the finds at the end of the palace style period, the 14th or 13th century BC, an era when the Mycenaeans had moved into Crete. While there are certainly several evidence that suggest animals were regularly sacrificed in the courtyard, I'm afraid we can't yet conclusively answer if the human remains also belong to a victim of sacrifice.