The term "Master Builder" is actually an official designation by the LEGO Company; per their website, "LEGO® Master Builders are the highly-trained and super-creative builders who design all of the official LEGO sets. Other LEGO Master Builders create giant, detailed sculptures out of LEGO bricks for LEGOLAND® Parks and special events all around the world."
The word "LEGO" is never once uttered.
In order to add more realism to the movie, the LEGO bricks have scratches, fading, and even fingerprints to make the movie look like someone was manipulating real bricks in a stop-motion fashion. The bricks are also affected by their locations, with the bricks in The Old West realm being more dusty and faded from the sunlight.
Vitruvius' (Morgan Freeman's) staff is actually a chewed up lollipop, and in most cases, the stick of a lollipop will fit a minifigure's hand.
Everything in the movie was designed to look as if built out of LEGO pieces. This even includes effects like water, fire, laser bolts, explosions, and smoke. For instance, the lasers are actually transparent LEGO rods (commonly known as "Lightsaber blades"), while smaller puffs of smoke are LEGO ice cream pieces. This is in contrast with the direct-to-video LEGO movies and cartoon series, in which parts of the sceneries and most of the effects were made to look realistic.