Some enigma operators had flourishes that the code-breakers could pick up on. Starting or ending a lot of messages with "Heil Hitler" was also a factor IIRC
Earlier in the war the Germans typically sent their call signs in plaintext. Many of the intercept operators in the “Y stations” in the UK became familiar with the “hands” of various German operators. Later in the war the Germans started encrypting their call signs, but Bletchley was generally able to distinguish them by the intercept operator’s familiarity with the “hands” of the German Morse operators.