These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Mac's stretching hands. Ugh. ET never tried anything like that.
The father alien twisting a tire iron into a knot, and later getting hold of a gun. It's easy to see why Phelous thought this would work better as a horror movie.
Rooting for the Empire: it's pretty easy to sympathize with the feds in this movie. Similarly to the Alternative Character Interpretation above, our heroes keep telling them that the aliens aren't going to hurt anyone, even though they've done almost nothing but cause mischief at the best and act like wild animals at the worst. Oh, and one of them gets hold of a gun. Any attempt at bringing them under control is justified.
Special Effect Failure: Mac frequently makes the sound of wheels moving whenever he moves, and then there's Eric falling into the river (where he turns into a completely immobile and obvious dummy), a scene Paul Rudd frequently showed on Late Night With Conan O'Brien.
As the supermarket explodes into an inferno, Eric is a cutout added in post!