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.
Creator's Pet - Debbie, who goes on to dominate many of the second season episodes, and is eventually the one who kills the lead Morthren in the season finale.
Fridge Logic - It's discovered in the first episode that the bacteria that put the aliens into hibernation is killed off by radiation. It looks the creators forgot that each one of the war machines had an UNSHIELDED nuclear reactor powering it.
Seasonal Rot: Most diehard fans tend to hold the opinion that the changes from the first to second season (which included the deaths of several major and supporting characters - including the villains of the first season, the world flipping over Twenty Minutes into the Future and most of the first-season plot threads dropped in favor of standalone episodes) caused the show's death.
Esoteric Happy Ending: During the course of the film, the implication is that a very sizable proportion of the human race has been exterminated and much of the planet has been laid to waste by the invaders. Yet with possibly millions/billions of people dead in the most gruesome ways and the earth in ruins, one gets the impression we're supposed to find the ending in which the family we've been following all somehow survive and reunite with the motherto be a happy one.
Then again, the aliens are all gone, and Humans Are Survivors. The world will be able to recover in time.
Faux Symbolism: When Ray and Rachel arrive in Boston, one of the first things they see there is a statue of a Minuteman covered in dying alien weeds.
HSQ: Spielberg keeps this as high as possible. One scene, a clever nod to the original story, involves a crowd of people, including our protagonists, walking through town, when a railroad crossing signal sounds. Everybody clears the tracks as the gate comes down. Then the train passes. It is on fire. It leaves, the gates go up, and it is not commented on by anyone. Roger Ebert, who gave the film a mixed but mostly negative review, called this scene "unforgettable".
The Scrappy: Robbie. His detractors point out he spends a lot of the movie being an asshole whilst seemingly wanting to get himself killed charging off into harms way. The fact his suicidal actions don't get him killed, and his survival is never explained, only annoyed his critics more.
Fans are often irritated by Rachel too, largely for being The Load.
The Woobie: Rachel, for those who weren't annoyed by her screaming. It helps that Dakota Fanning gives an excellent performance.
Ray has his moments, especially when he's realizing his shortcomings as a father.