There were absolutely cover ups by the FBI, CIA, DPD and SS—all of them screwed up in their areas of responsibility, they had a lot to be embarassed about. They all knew in retrospect that they had not been vigilant enough, and it cost JFK his life.
Yours is a plausible explanation. They all had a file on Oswald and didn’t act on them. At the time, the American people were out for blood over the assassination, which was a main reason for the Warren Commission. They had to give a straight, credible answer to the American people and maintain credibility of our government institutions.
The commission no doubt had all this information and chose which to reveal and conceal in what they perceived to be the country’s best interest.