The reason why Lee Harvey Oswald had so many connections to people related to the CIA and to those with QKENCHANT clearance provided by the CIA is that he was to provide countersniper duties to protect the President. No one expected he would assassinate the President.

There had to be a coverup because of Soviet disinformation, any ambiguousness would be seized upon by the Soviets. Some JFK investigators had communist ties and links. Weisberg for instance was blacklisted by the FBI from making FOIA requests because of his Communist background that he was fired from the State department for. https://jfkresearch.wordpress.com/category/harold-weisberg/

This was a well meaning coverup. The CIA and the FBI are not responsible for JFK's assassination.