Agreed... it's most likely an irritation caused by the chlorine in the pool. How fast/hard are you swimming? Are you getting your heart rate up and thus, your breathing rate? It's probably just me, but I tend to get a sore throat from strenuous cardio workouts that make me breathe hard & fast. I live to CO so I'm guessing it has something to do with the dry air.
I'm just thinking that in your case it might be a combination of breathing harder/faster/deeper that you normally do combined with an influx of chlorinated water hitting the back of your throat. Something you might try to work on is rotating your hips more, so your mouth is further out of the water when you take your breath. This may/may not help minimize the amount of water splashing in and around your mouth & lungs. Just a thought.
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