In 1775 campaign when they arrive Howe and Clinton both have seniority of 3 which leads to clinton assuming the command of the forces by default if both of them are in the same stack (even if the picture of the stack shows Howe as commanding Clinton will be the one in charge during the turn resolutions). Which is quite bad considering his -4 CP penalty when commanding - so your forces can end with a out-of-command penalty.
The situation is resolved when Howe is promoted to commander-in-chief by an event but couln't you simply lower Clintons seniority to 4.