The article says: "Europol said that French police had discovered some of EncroChat's servers were located in the country, and that it was possible to put a 'technical device' in place to access the messages." Even if it was end-to-end, they at least could intercept the initial key exchange perhaps.
Intercepting a DH key exchange doesn't help you. The whole point of DH is that an eavesdropper doesn't learn the secret even though both of the other participants do.
They probably just didn't use end-to-end because it's easier to offer a nice customer experience without.
