Champaran HumSafar Express : इन अजनबी सी राहों में, जो तू मेरा हमसफ़र हो जाये, बीत जाए पल भर में ये वक़्त, और हसीन सफ़र हो जाये. - Piyush Singh

Reason can be many, but exact reason would be known to rare!!
Probable reasons:
1. Land Acquiring & alignment, leading to distant Track Diversion & Station getting further away!!
2. City wouldnt have been prominent @ Track-Lay Era, which later would have got prominence!!
3....
more...

Geographical Constraint - Hamirpur dont have main station, but have Hamirpur Road, some 15 Kms away, as Hamirpur lies in between Yamuna & Betwa Confluence)
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PS: There lies infinite stations which are far away from main city & the station been named X-Road!!