One HomePod buyer claimed online the speaker "left rings on my wood furniture in less than 20 minutes of use". Reviewers Pocket-lint also confirmed how quickly the damage could appear.
Apple has acknowledged the problem on its customer support page, but so far its only suggestion to tackle the problem is to move the speaker.
"It is not unusual for any speaker with a vibration-damping silicone base to leave mild marks when placed on some wooden surfaces," Apple said.
Apple said the marks should disappear over several days, and if not "wiping the surface gently with a soft damp or dry cloth may remove the marks".
Read more: Apple admits 'coldgate' bug with iPhone X screens
It added: "If you're concerned about this, we recommend placing your HomePod on a different surface."
The HomePod was billed as Apple's high-end answer to Amazon's Echo smartspeakers, powered by its Siri virtual assistant to provide voice control, read the news and answer questions, as well as providing access to millions of songs.
It's not the first design flaw from Apple's new products. The company recently told its engineers to scale back the rate of updates for its iOS 11 software to avoid a string of bugs that have been found in recent updates.