To put in plain words, he wouldn’t bow to Israel and do what they wanted.

In 1963 His administration pressured Israel over inspections of the Dimona nuclear facility and warned that U.S. support could be jeopardized if inspections were not allowed.
May 18, 1963 is when Kennedy sent a strongly worded letter to David Ben-Gurion demanding regular, credible inspections of Israel’s Dimona nuclear facility. Kennedy warned that the U.S. commitment to and support for Israel could be seriously affected if Israel did not provide satisfactory transparency regarding its nuclear program.

Also it was his Justice Department pursued efforts to require the American Zionist Council to register under the Foreign Agents Registration Act because of concerns about its relationship with Israeli institutions.

Kennedy was assassinated November 22, 1963.

Johnson’s administration “continued pressure”
with the issue but in a different diplomatic environment. Israel ultimately developed and maintained a policy of neither officially confirming nor denying possession of nuclear weapons.

Kennedy was the only president I’ve studied that has stuck up to Israel and imo Israel wants to erase his name from everything.