Can you provide pictures of what you found?
And yes, it's perfectly possible your snake was incorrectly sexed when you bought it and that it's now laying infertile eggs. It's not particularly common, but it's not exactly rare either.
Go ahead and take whatever it is out of the tank, it won't distress your snake. That said, however, eggs would not cause breathing difficulties and they aren't normally visible as 'lumps in his side', so a vet visit is still definitely in order.
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