For instance if you get a point when you click with and item, and in the end of it, the item is taken away then there seems little point to check a flag. Likewise if you interact with a view which results in the view disappearing, again no reason to check a flag.
I have already had to bump up the number of flags that the game makes use of, in some cases like those mentioned I don't need a flag, just to up the score.
As far as it being a bug in SQ5, I checked kq5,kq6, sq5, and some other game, can't think of it now but the changeScore wasn't used in any room and the SL doit method of game was identical in all. I wrote up a quick tutorial adding a ChangeScore procedure... Is this lil bug something that you are going to squish for the final release? If so, I'll rewrite the first add to player score tutorial to show both methods and ditch the modification tutorial. If not, I'll probably just leave them as is.