Hola Javier!
I'm not sure I've got your question, but Wwise doesn't automatically loop a music segment. If you want to loop then just switch your Layout to Interactive Music and on the bottom of the screen, with your sequence or random container selected, you'll see a playlist (or you can set up one if you haven't already).
One of the reason to not automatically loop a music segment is to allow musical stingers for example. Stingers are bits of music that underlines a specific action, such as killing a powerful enemy or triggering a special skill.
The transitions are managed by the transition matrix. You can find it by clicking on your music selector switch and then in the Transition Tab. I suggest you to work with it using the Interactive Music layout.
Let me know if this helps.
Hasta luego. ;)