Several types of wirings at the 35 kV side are carried out in the practical 500 kV substations. Breaker rear-wiring is often adopted in the 35 kV reactors intervals of 500 kV substation which was put into operation earlier. This type of wiring can save cost to some degree. However, it can cause secondary side problems. Based on a practical instance of 35 kV reactor failure in a 500 kV substation in East China, the secondary side problems, including failure of fault phase selection, misoperation of undercurrent protection and no-returning after protection operation, caused by the breaker rear-wiring are analyzed. Finally, the corresponding countermeasures are provided.