The whole "arriving by boat" thing seems just odd. There are so many easier ways of getting into a city like Bombay such as road, rail etc where you are less likely to be stopped and searched. There's simply less sea traffic than road traffic; you stick out much more if you're in a boat.
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Probably they were trying something that no one was expecting ...... you are not a terrorist so you cannot think like one .... now we all know it is a possibilty. Again i would say these are just speculations and let us watch how it unfolds.