It is a dark filter for a dark movie but if you watch with a clear mind you will be pleasantly surprised by how many beautiful and "full-of-light" scenes exist. Apart from our low-profile protagonist, whom you can sympathise, the friendly chubby baker is a perfect character with which you can relate. As a character, he sees magic as a whole from his "non-wizard" perspective so the viewer can have an easier way to understand this magic world.
Now to the fun part. When did all the creatures escape his suitcase? I am sure someone would see a rhino-sized creature escaping a magic suitcase. Why the woman who is able to read thoughts did not know that our protagonist wanted to leave the house when her sister brought the men some hot cocoa? Finally, how long was that night? No-one ever sleeps? Does the ministry of magic work 24 hours a day? Apart from the plot holes, it is a bit of disrespect to the magic world the fact that "hand-waving" move heavy objects. This is not Star Wars!
Plot holes are not that important compared to the lack of interest of the main villain during his dark moments with the charismatic but troubled young man. It is a fun theme that tries to fuse with the rest of the magic world. Trying to mix a story of magic creatures and the story of a darker ministry situation is tough but it is not implemented satisfying enough unfortunately. As feelings grow for our friendly caretaker, the viewer is focused more on the "fantastic beasts" part of the movie and the funny adventures with our chubby-baker which by the way nailed his job as a comic-relief. A deeper story exists which is also interesting but in the end you do not what want to watch the movie for.
In the end, you have a sweet taste. All end well, the villain is caught and our protagonist does not go to jail. Of course even if some "mistakes" need to be pointed out, the sweet taste is what matters.
"Jacob: Newt... I don't think I'm dreaming. Newt: What gave it away? Jacob: I ain't got the brains to make this up."
"Jacob: Tell me, has anyone ever believed you when you told them not to worry?"
"Newt: See, they're currently in alien terrain, surrounded by millions of the most vicious creatures on the planet. Humans."