Unless there is a malfunction with the firmware of the camera or the contacts with the batteries, the most probable cause is, that the batteries are indeed counterfeit.

Currently there are not only 3rd party batteries out there, there are also a LOT of counterfeit batteries, which look astonishingly close the the original including hologram logos, packaging etc.

Usually that starts an arms race between the manufacturer and the party creating the fakes about detection. Better detection methods usually come with a firmware update of the camera, so suddenly formerly trusted batteries are detected as counterfeit.

Using them is a bit like a leap of faith - I am using a known counterfeit in my Sony, which is currently not detected. And the battery performs just as well as the original. However, if that battery swells or start burning and you would take claims to the manufacturer, you are on your own.

To make matters worse, Canon also had issues with counterfeit detection before on their ink cartridges and mis-detected counterfeits there.

My advice would be: If you paid full price for the batteries, I would have them checked. If you can live with uncertainty, the message is just irritating, but does not come with any other implications.