A method and apparatus are disclosed. In an example from the perspective of a User Equipment (UE), the UE receives one or more signals indicative of a first Physical Uplink Shared Channel (PUSCH) and a second PUSCH on a first cell and in a Transmission Time Interval (TTI). The UE determines to transmit a first Uplink Control Information (UCI) in the TTI, wherein the first UCI overlaps with the first PUSCH and the second PUSCH in time domain. The UE selects the first PUSCH for multiplexing the first UCI based on whether the UE is configured with joint Hybrid Automatic Repeat Request (HARQ) feedback mode or separate HARQ feedback mode. The UE transmits the first PUSCH and the second PUSCH on the first cell, wherein the first PUSCH transmitted on the first cell includes the first UCI.