use other conditions/selectors, like:
Global variable (paused = 0, set it to 1 when paused, set back to 0 when leaving the pause, add a condition to popping the bubble: paused = 0 so that it is only possible when the game is not paused)
Deactivate an event group when pausing, so that the events in that group are disabled. When you continue the game, the group should be activated again.
If you have problems with the z-order, just put the stuff that is supposed to overlap the bubbles to a layer above.