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.
Gribble: I was a good kid. Followed orders, put my toys away. That's why they took her, because of me. What kind of message is that to send to a little kid?
Inferred Holocaust: Oh, sure Milo saved his mother and got home but there's the small issue of the evil fascist regime that's been in power on Mars for decades. During which time they've been casually throwing baby males into the garbage to fend for themselves, training the females to be unquestioning enforcers, executing dissenters and murdering countless human women. All apparently carried out by Martian society at the whim of one individual's insanity. The past evil deeds and problems facing Mars are unlikely to be instantly solved by revealing society was built on a lie. Somewhat averted in that they have Gribble and Milo (and his mom) to guide them through the internet connection.
Tear Jerker: The fate of Gribble's mother. Not to mention how distraught he was when he was telling Milo.
Uncanny Valley: As this trailer demonstrates, the movie possibly surpassed The Polar Express in terms of creepiness. It doesn't help that they used an actual kid for the voice but based the motion capture off of Seth Green, hence the dissonance. And the baby Martians, oh man, those baby martians.
Unfortunate Implications: As the Something Awful review points out, the Martian women have assumed positions of power that have left them completely unable to care for Martian children (as there's no way someone can hold a full-time, influential job and be a loving mother at the same time), the Martian men have become effete layabouts as a result, and the movie directly says that Martian children will only truly thrive when raised by a mommy and daddy (and anything other than the traditional nuclear family isn't capable of raising children). It's like someone adapted a parenting book from the 1950s.
The hype makes it sounds like a comedy, but the kidnapped mothers get their brains drained before being vaporized. No wonder Gribble didn't want to tell Milo the truth behind why he's on Mars.
Milo's mom almost gets vaporized to provide memories for the new generation of Nanny-Bots, then Milo gets shot in the foot with a laser and suffers not from excessive blood loss from GETTING SHOT, but will now die because his helmet broke, and then his mom pulls a Heroic Sacrifice to save him, dooming her. This also spawns some Fridge Brilliance.