CX non-full fares usually have routing restrictions. For MNL-SHA, the routing allowed is probably MNL-CX-HKG-CX-SHA. By forcing an extra stop in KUL, you have to upgrade to a full fare, which is usually based on maximum allowable distance (no routing restrictions)

Best option for you is probably to get PVG-HKG-MNL, an open jaw at destination, and KUL-HKG-PVG.

CX is a single hub airline, so they use routing based fares a lot. This is in contrast with, for example, AA, which has multiple hubs and usually their fares are based on MPM and have a ticketed point reduction at certain hubs