Apple has a history of removing items from shelves in order to make way for similar items for sale. An Apple spokesman did not comment directly on the reports, but in an email to CNBC said, "We regularly make changes to the merchandising mix in our stores."
In an email, a Nest spokeswomen declined to share details about the reports but said their products will still be available through Apple in the coming weeks.
Meanwhile, Apple is now selling a different wireless thermostat, the Ecobee 3—one that happens to be a direct competitor to Nest, which is owned by Google. The Ecobee 3 works with Apple's HomeKit, an operating system for internet-connected home appliances.