Hello Harry,
I’ve tested on my side, and there is no such issue.
I set 3 wakeup sources as WKUP0, 1, 2 (MSCR43, 146, 148) and enables those by WRER.
I tried to wake up by WKUP0, and successfully waked up and the WISR value was only source 0 like below.

Please refer to below register setting that I tested with.
WKPU_WIFER = 0;
WKPU_WBMSR = 0x00000007;
WKPU_IRER = 0x0;
WKPU_WRER = 0x0;
SIUL2_0.MSCR[43].B.PUE = 1;
SIUL2_0.MSCR[43].B.PUS = 1;
SIUL2_0.MSCR[43].B.IBE = 1;
SIUL2_1.MSCR[146].B.PUE = 1;
SIUL2_1.MSCR[146].B.PUS = 1;
SIUL2_1.MSCR[146].B.IBE = 1;
SIUL2_1.MSCR[148].B.PUE = 1;
SIUL2_1.MSCR[148].B.PUS = 1;
SIUL2_1.MSCR[148].B.IBE = 1;
STBY_GPR.WKUP_PUS.B.WKUP_PUS |= 0x1;
WKPU_WIPUER_WIPDER = 0x1;
STBY_GPR.WKUP_PUS.B.WKUP_PU_OVERRIDE |= 0x1;
WKPU_WIFEER = 0x00000007;
WKPU_WIREER = 0x0;
WKPU_IRER = 0;
WKPU_WRER = 0x00000007;
WKPU_WISR = 0xffffffff;
Best regards,
John