This warning could have for sure been sparked because Malta is seen to take away business from the rest of the countries in EU, when it comes to regulated/licensed bitcoin businesses, while the warning about AML may only be what's happening on the surface.
Malta is not taking away businesses from other EU countries simply because those businesses wont be in other countries because other countries have much stricter regulation. It is a miracle that EU has not imposed some stricter rules on Malta . There are a lot of big crypto exchanges registered there Binance,Okex, Etoro and most likely more.
Eu is just concerned the huge amounts of money going thru there unregulated.
Actually, it may have been a valid cause for concern, not necessarily restricted to Malta but to all these tiny "blockchain jurisdictions" formerly known as tax havens for complicated tax structures.
It's not really so much of a secret that the world stood by and allowed all the money to flow under their eyes and under the radar for so long. Now that they cracked down on it, it's only fair they extend that restriction to all forms of new money. For them bitcoin/crypto's just a new vehicle. They see it exactly as a new financial tech, and when you have clients now