Hello! Usually if in layout name 1 net and in source name - 2 nets , it means that you shorted PWM_B,X123/PWM_B. Have a look carefully, may be you put extra some vias.
As life huck you mean put some pin (for exapmle "name1") on net PWM_B and pin "name2" on net X123/PWM_B and then LVS will see shorts and it will be easier to find short.