I could think of a few.

~Someone misses ferry and has to wait for next one. (Rustboro, Dewford, Slateport, Lilycove, Mossdeep, Sootopoolis, Pacifidlog)
~Arguement and someone leaves temporarily (Jacob and Magnus aren't always gonna get along, as are Jon and te rest of his team.
~Forced to flee a fight from team Aqua and Magma, and accidentally gets seperated.
~Interns get given a bit of free time during their stay in a certain city.
I will think of others later if we need them. It would be easier to explain why they aren't with the group than why they suddenly have a rare Pokemon/item (quest reward)