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.
YMMV: Even Dwarfs Started Small
True Art - There is definitely an undercurrent of Art Film-ness in the film, though it avoids the usual.
Unfortunate Implications - One could be forgiven from assuming the message of the film is "Gosh, aren't little people wacky and weird and not like normal humans at all?" The only person who behaves anything like a recognizable adult is the Headmaster. Herzog may not have intended it, but there's a strong argument to be made that the film does a good job of Othering those who have physical disabilities.