Abnormal low-frequency lateral vibrations of the carbody present a significant issue in commercial train operations, severely affecting passenger comfort and potentially compromising operational safety. This is usually linked to carbody hunting, triggered by low equivalent conicity early in the wheel re-profiling cycle. However, in this study, it was observed during the later stages of the wheel re-profiling cycle in conjunction with atypical wear patterns in an intercity EMU train. To investigate the underlying causes, a long-term experimental study was conducted, tracking both carbody vibrations and wheel profile wear. A detailed vehicle dynamics model was developed to analyze the mechanism behind the phenomenon. The study identified that the combination of high hardness in the abrasive blocks of the tread cleaning device, high-pressure continuous operation, and the frequent start-stop cycles characteristic of intercity trains collectively contributed to the development of a double-hollow wear pattern on the wheel profile. This wear pattern reduced equivalent conicity, leading to carbody hunting phenomenon, resulting in a 1 Hz lateral harmonic vibration. To mitigate this issue, the hardness of the abrasive blocks was reduced, and their operation mode was adjusted to low-pressure intermittent operation. Validation through a subsequent re-profiling cycle demonstrated that these modifications effectively shifted the wheel profile to a single-hollow wear pattern, increased equivalent conicity, and prevented the recurrence of abnormal vibrations. This research provides essential insights and practical solutions for railway engineers seeking to mitigate carbody hunting, thereby enhancing operational safety and passenger comfort.