It read the .env file after I created it from the example, spreading its contents into many places.

Unfortunately, the .env anti-pattern is endemic throughout many projects, and whether Claude creates the .env from scratch or merely the .env.example, it will end up feeding the .env back to Anthropic with enough interaction, apparently. And developers should expect all files in their work directory to be read by Claude, that's not so much a fault of Claude as it is with the .env anti-pattern.