The GUI of the computer in Flint Lockwood's lab changes from either a Unix / Windows interface, with restore, minimize and close icons on the windows on the right initially. However, when his dad sends the email, the GUI is a representation of a Mac OS with the icons on the left and in standard Mac OS colours.
(at around 1h 10 mins) When the clouds are seen approaching Manhattan, the city can be seen. The Empire State Building is located in Upper Manhattan, but yet is portrayed as being in Lower Manhattan, almost near what was then Ground Zero.
(at around 47 mins) The dam that prevents the leftovers to flood the city with uneaten food is arched the other way around. An arch dam built that way would collapse instantly as soon as any load is applied.
(at around 23 mins) The FLDSMDFR breaks the water molecules to hydrogen and oxygen, and recombines them to create bacon. However, food consists mainly of carbon, which can be derived from water only by nuclear fusion, and it can't be done by the machine microwave energy.
(at around 51 mins) When the screen cuts away to the Cities Weather Forecast, several cities listed have anomalous weather readings. Some have extremely cold weather with a rain cloud next to them (if it were that cold, any precipitation would be snow), and some have mild temperatures with snowflakes next to them.