There has never been any confirmed evidence that Mark Harmon actually disliked Michael Weatherly. Most of what fans discuss comes from behind-the-scenes rumors rather than verified facts. The two actors reportedly had very different personalities, with Harmon known for being more private and serious, while Weatherly was often described as playful and spontaneous.
Because of these differences, some people speculated that they did not always see eye to eye on set. However, despite any contrasts in working style, both actors remained professional throughout their time on NCIS. They worked together successfully for many seasons, and there has never been any public confirmation of a serious conflict between them.