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This "dip" in the hull is common and natural in many kayaks. It also occurs with age, as boat hulls tend to wear in the seat area. This area under the seat is no less strong than the rest of the boat, but it is less rigid due to the large, flat area. Therefore it can buckle due to temperature fluctuations, pressure from tie down straps, storage conditions, etc. This should not be considered a problem unless you notice an extremely soft or spongy feeling when pressing on this area. The same is also true of dents in the side or chine of the kayak.
These are often noticed after the boat is removed from vertical transport on a roof rack. The solution is to set the boat in the direct sun for a couple of hours (preferably in a grassy yard, not on pavement) with the dented area exposed. When the hull heats up it usually reforms itself. You may have to get creative with some weights or braces inside the boat to push the dents back out.
This process should be allowed to proceed for at least two hours. In the absence of sun or in the cooler months one foolproof way to not damage your boat and remove a dent is to use water that has been brought to the point of boiling. This will heat the plastic to a soft state without burning or melting it and allow you to push the dent out.