That Burana Minaret is still included in the former TWHS although subsumed is a mistake.
The reason Spoleto and Tempietto sul Clitunno is still there is, as Solivagant duly noticed, that not all of Spoleto has been inscribed. Maybe it would be helpful to have an attached comment about the inscription of a part of it. Examples of similar cases are relatively common:
prehistoric sites (Israel), prehistoric sites (Cyprus), Olomouc (Czechia), Kezmarok (Slovakia), Cefalu (Italy), Cividale (Italy), Gargano (Italy), Piedmont vineyards with Valtellina (Italy), Palermo with botanic garden (Italy), Thessaloniki including ancient monuments (Greece), Athens (Greece) Franciscan monasteries of NE Brasil (Brasil), Malpelo and Gorgona (Colombia), Isfahan (Iran), Oaxaca with Cuilapan (Mexico), Puebla with Cholula (Mexico), Nan Madol with Lelu (Micronesia) and Pecs (Hungary).
I am pretty sure I missed some.