Query regarding self-owned shop.

My father owns a tyre shop alongside a highway. This area was supposed to be a godown and not meant for a shop. This was not informed by the person by whom my father bought the shop. Like him there are other shop owners in the same building who were unaware that the building where the shop is present is supposed to be a godown. They all like my father owned their respective shops since the past 24-25 years. Now, after so many years, suddenly the municipality is troubling them and threatening them with warrant to seal their shops if they do not stop doing business there and use the shop premises only as a godown. All shop owners including my father got a stay from the court against that seal warrant. So, recently the police issued arrest warrant against all shop owners urging them to get bail. Kindly please advice as to whether it is legally right practice to wrongly target the shop owners who were not aware at the time of buying the property that the shop premises was a godown area and have only come to know about this fact recently.