Is it possible it's been there all along? I had a bubble when my pool was filled rapidly (firehose) years ago but luckily was on the wall. Because it was filled so fast the bubble didn't escape and they vented it up the side. I'm thinking you have an air bubble, and a tough one to get to.
Edit: I don't think it would hurt anything to leave it, but if I were you I'd call the experts to vent it. It's easy to vent the sidewall but getting below that would be tough.
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