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.
Alternative Character Interpretation: While Brainard himself seems to believe otherwise, it isn't too much of a leap to wonder if he might have a genuine undiagnosed memory disorder, especially considering the early scene where he's clearly having trouble recalling that he's even engaged, and that the rehearsal was the previous night.
Designated Hero: Professor Brainard is supposed to be "comically" absent-minded, but just comes off as a self-centered jerk.
Esoteric Happy Ending: The ending with Braniard attending wedding #4 from his lab by video proxy was supposed to be a cute, fitting end to the movie. Didn't quite work for many people.
Fridge Horror: Flubber is a sentient substance capable of flying without effort and of increasing in energy after bouncing. What is the definition of an Eldritch Abomination? According to TV Tropes: "The Eldritch Abomination is a type of creature defined by its disregard for the natural laws of the universe as we understand them."
Also, Brainard uses Flubber to make cars fly. This means that Flubber must be held in the vehicle for years, unable to do anything it wants to, with no socialisation.
Fridge Logic: How Weebo can fly before Brainard invents the Flubber hover technology? And why wouldn't this work with cars?
Weebo in general create numerous problems because the technology is so fantastic. Not the least of which is that why, if the professor has basically created an emoting, flying AI with vast uses and abilities, does nobody think to sell her or her technology for the money to save the college? Naturally, the original film did not have this problem - Brainard just had a normal, non-talking dog that he tended to explain stuff to so the audience wouldn't think he just talked to himself for the hell of it.
Dr. Brainard forgot his own wedding three times (at least twice). Even if this was before the age of cell phones with schedule functions, he couldn't invent a wacky reminding machine? Or used a post-it note!? Sure Weebo kept sabotaging his attempts to keep schedule because she loved him, but you think he'd have had more important ways to remember the wedding. Or certainly he could have just made sure someone from the wedding party, like his best man or his parents (or her parents or his friends) just called him or...
Roger Ebert brings up this very topic in his review of the film. Though early in the film, Wilson openly states that he steals all of Brainard's creations and profits off of them, there's still a number of objects in his home that he clearly could have sold on his own (like Weebo!)
It's explained that Brainard has tried but can'treplicate the technology that created Weebo and is his only remaining creation, not stolen by Phillip's rival, Wilson. The only plans to a her, in the form of her "daughter", only appears in a video will after her "death". On the other hand, the idea that he could create life and never replicate it is hard enough to handwave with "Weebo hid it" when he presumably would have written things down by hand.
Informed Wrongness: Despite the fact that Phillip has just blown off a third wedding ceremony due to his absent-mindedness, the movie attempts to make it look like Dr. Reynolds' Tranquil Fury response - and subsequent breaking things off - to his half apology/half "But look at this cool thing I made" exhibition was an emotional overreaction.
Mis-blamed: Some of the particularly obnoxious plot elements, including abandoning Sara at the altar over and over, are carried over unaltered from the original film. Of course, one could still criticize this film for not fixing them in the first place.
Replacement Scrappy: The original film featured the Professor often talking to his non-sentient dog when he needed to infodump on the audience. The remake replaces the dog with Weebo. While she's not exactly a hated character, the existence of a sentient machine completely trumps the invention of Flubber if the audience thinks about it.
Squick: The entire subplot with Weebo's lust for the professor, progressing into creating a sexy female hologram so she can act out her emotions for him physically when he's asleep, and finally the admission at the end of the film that upon her death, she gave Brainard a copy of her design called "our daughter" - with modifications based on both Weebo and him. In case the analogy hasn't bludgeoned you hard enough, Weebo's final thought that allows Brainard to find the file? The word stork.