The dispute originated with Mr Bier, who accused the Commission of activating a rarely-used account “to take advantage of an exploit”.
He claimed it had posted a link which itself deceived users – tricking them into thinking it was a video “to artificially increase its reach”.
He said the “exploit”, which had “never been abused like this”, had now been removed.
Ad accounts on X are used by businesses to create and analyse paid advertising campaigns and run “promoted” posts on the site, separate from the users’ X profile.
In response, a European Commission spokesperson told BBC News that it was “simply using the tools that platforms themselves are making available to our corporate accounts”.
“We expect these tools to be fully in line with the platforms’ own terms and conditions, as well as with our legislative framework,” it said.
And it is not the first time there has been disagreement between X and global regulators.
In 2024, Brazil’s Supreme Court lifted a ban on X after it agreed to pay 28 million reais ($5.1m; £3.8m), and blocked accounts accused of spreading misinformation.
The previous year, Australia’s internet safety watchdog fined it A$610,000 ($386,000; £317,360) for failing to cooperate with a probe into anti-child abuse practices.
