There were a number of latent and semi-smudged prints on the rifle but the FBI examiner was an old-school stickler requiring a certain degree of lift quality and number of identification points. For a print to be considered for lifting at the FBI then, it had to be visible on the object with enough points through a hand-held magnifying glass.
It probably worked in the defendant's favor that the FBI could have (but in this case, did not) document partial and smudged prints on the rifle. People just assume that the FBI would necessarily be more advanced than city crime labs. See Peter principal as to why the FBI might have a by-the-book stickler doing fingerprints (Latona had been with the FBI for over 30 years by 1963).
Latona dismissed the trigger-guard housing fingerprints as "of no value" despite his own efforts to photograph them and having Day's photos. It was not until 1993 that the trigger-guard prints were better analyzed by combining the high-quality pictures taken by Day. The results were presented in the outstanding 1993 PBS documentary "Who was Lee Harvey Oswald?".