Speaking of "levels", do you mean Contruct's layouts, or your external levels, which loads into single "playground" layout with a number of included sheets and events? If so, try load every single level in separate layout and include events only specifed for this level.
I mean, if you load, for exemple, "level 1-1", and layout which load that level has included sheets like "level 1 Boss", "level 2-2", etc., it probably will use extra CPU even if it doesn't perform any actions (well, as I think)