When you pause the game and use actionLists (for menu interactions for example) if you had some audio playing, you can hear a small bits of the audio when you execute an actionList. I did some troubleshooting and it seems than AC GameState switches to cutscene for a short moment when activating an actionList. And since AC GameState is not Paused anymore, the AudioSource.pause = false gets called and you can hear a short moment of the audio. During this entire procedure Time.timeScale seems to stay at 0, so checking against timescale instead of GameState might be a possible solution. Should be around the StateHandler.cs 363 line.
Comments
Be sure to check that Unfreeze pause menus? is set to Off in the ActionLists's properties. That should ensure the game never reverts the timescale.