One child appears to be locked up in his room or house some/most of the time, but the situation is unclear. We do see him play outside, so it's sort of confusing.
Spoiler: There is a mention that Klaus's old wife, Lydia, died of an unspecified illness. She wasn't a parent (in fact, that's kind of what makes this even more upsetting), but I still want to point that out.
Spoiler: Klaus's wife is indirectly mentioned to have died from a disease. Although the illness is never specified and it's fairly unlikely that it was from cancer, I still feel like it's important to mention.
They aren't used, per say, but one front yard has spikes in the front to ward off neighbors (no one actually touches the spikes). Being an animated movie, the spikes aren't realistic. The scene with the fish shop and meeting Klaus for the first time also has some hooks present (again, not used).
No explicit hate speech, but the main character does ask "What's wrong with her mouth?" when he encounters someone speaking in a foreign language. It seems to be more of a misunderstanding than trying to be offensive, however. (Some languages simply change the line to "What is she saying?")
Perhaps a hint. One character thinks another character's behaviour is crazy, but since he's afraid of him, he says, "Wow... That's... totally normal! Not a sign of any mental illness or anything" - obviously really being of the opinion that it must be.
Homelessness is mentioned, the main character is cut off by his father financially and his father suggests if he fails he'll end up "in the gutter." This is referred to a couple times.
Klaus takes a very comfortable and sweet view of the Santa mythology.
Could be argued that showing Santa as a once living man might spoil certain beliefs of the Santa myth. Overall though very sweet and true to the feeling of Christmas and Santa