Polyethylene is by nature soft and indentations in the hull are common for a number of reasons (pressed against another kayak while in the container, tied too tightly onto the roof racks of your car, inappropriate storage racks etc.)
You can reduce the chance of indentations appearing by using a kayak cradle on your roof rack rather than just strapping the kayak to the straight bars and using a wall rack, wall sling or hoister system rather than storing the kayak on top of uneven surfaces.
Because the plastic has memory these indentations can usually easily be removed by either leaving the kayak upside down in the sun or inserting a piece of closed-cell foam into the kayak directly above where the indentation appears and leave it like that overnight. Applying a hair-dryer or hot water can also assist in more extreme cases.
The important thing to remember is that indentations in the hull are common across all models and all brands of polyethylene and HTP plastics, but will not impact the performance of you kayak at all.
If this bothers you then you are better off getting a fibreglass or thermoformed ABS plastic kayak (such as Hurricane or Barracuda Beachcomber) as these materials do not form indentations on the hull, however, remember that fibreglass (including carbon and kevlar) are not as durable as plastic kayaks. For durability combined with excellent hull shape retention thermoformed ABS plastic is your best option.