Well seeing as you are using a global array instead of the actor*s (which would probably be a better method), you would have to set the subs of the array to some xy value not attainable by the actor. Just put aside a x value, in this case -999, and in destroy set it to that value.
alien -> Destroy Actor -> Script Editor
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aliens[me][0]=-999;
And in the canvas actor, check if the aliens[i][0]!=-999, and if so create the dot.