you said something that is not making sense :
“same UARFCN but different frequencies”
Could you please be more explicit ?
In one sector with several carriers (1 cell per carrier), all those intra-sector cells can use the same SC. And it is what is done, all the time. So using the same SC on different cells of the same sector is normal, as long as each cell is using different frequencies (FDD1, FDD2, FDD3, etc)
How is the QoS in those 2 cells? How is the SHO success rate ?
Have you run your SC check in the neighbours of the neighbours ? That’s usually how the alarm is triggered : the neighbour of a neighbour is using the same SC.