The main difference is in the primary use of space. A settlement is usually considered to be a place where people reside. It's where people live and sleep and eat and spend their free time. Villages, towns, camps, cities, all are settlements.

A "sanctuary", on the other hand, is a place that is not primarily used for dwelling, but is a gathering place used for some sort of communal purpose, such as worship, communal feasting, rituals or ceremonies, etc.

Çatalhöyük is a settlement, because it consisted of lots of houses, where people lived.

Göbekli Tepe is not considered to be a settlement, because people do not appear to have resided at that site full-time. They did not "dwell" within Göbekli Tepe. It was not their home. They do appear to have gathered there at frequent intervals to fulfill some social or religious purpose which is yet to be fully determined. Leading theories include ritual feasting (perhaps for a religious or social purpose), or perhaps funerary rites, or for worship. But it was not used as a "home", unlike Çatalhöyük, which featured lots of individual houses complete with sleeping areas, cooking areas, and all the other activities one would associate with a place in which people dwelt.

That's the main difference between the two classifications.