Actually Bill Williamson and Javier Escuella do become Arthur's enemies. When Bill and Javier side with Dutch and Micah they were ready to fight and shoot Arthur and John later in the stroy.
Later in the game there are also random moments around camp Bill and Javier walk up to Arhtur questioning his loyalty to Dutch. They also ask for Arthur to stop questioning Dutch's actions. There is a moment when Arthur and Charles are talking to each other and Bill wants to know what they are saying. Bill believes they Arthur and Charles are betraying Dutch so with all that evidence yes Bill and Javier started becoming enemies to Arthur Morgan. Infact before they side with Micah Bill and Javier start to get mad angry at Arthur during their conversations.
As for Joe and Cleet they are friends with Micah they joined the gang later on. When they joined close to the end of the story mode Joe and Cleet were not friends with Arthur they were strangers he didn't know.