The US has regularly had to deal with allies and partners whose interests clash with it. I’ve previously highlighted the problem America faced with South Vietnamese (and Thai) interference in Cambodia in the late 1950s – at least some parts of the USG wanted GVN and the Thais to back off on their border disputes with Sihanouk’s Cambodia and links with anti-regime dissidents, but Saigon and Bangkok were crucial to other American interests.
Another version of this dilemma can be found in Taiwanese backing for anti-CCP forces in northern Burma/Myanmar in the 1950s. The Taiwanese pulled forces out under pressure in 1953-54, but got back to it in the late 1950s (also with Thai backing), much to American chagrin. This is a useful analytical paper by the State Department in February 1961 laying out the leverage problem and a possible way forward (which ultimately mostly worked):
Paul Staniland 