I assume that when this happens that the "Back to Arrangement" button/red light on the top of the screen is lit. If you press that button, the red light will go away, and playback will be based on what is in the arrangement view.
you can have sounds playing simultaneously between the Session and Arrange views, but only one sound per Track number at a time. For example, if you have a sound playing in track 3 in the arrange view, and then launch a clip in the session view's track 3 column, the arrangement view track will be greyed out, and the Back to Arrangement light will come on.
To help work around problems with tracks being greyed out, I've made a point to always put clips in the same track number as they were in the session view originally. This is also good to remember, as any effects devices will affect the same track whether in the Session or Arrange views.
hopefully this solves your problem