A black lake filled with dangerous creatures. Place a safety barrier around the lake, with clearly signposted safety information
A wooden bridge that can catch fire in an accident. Demolish and build a new bridge made of stone or have anti-inflammatory charms to be placed on the bridge, with fire extinguishers placed every 15 metres
Peeves constantly causing trouble. Exorcism or have the Bloody Baron kick him out.
Books that can come to life, such as the Monster Book of Monsters and the Screaming Book. Clearly signpost all living books, and how to interact with them.
Abusive teachers like Snape and Umbridge. Remove abusive teachers from workforce pending a conduct investigation.
Moving staircases which can make things difficult to navigate the school. Moving staircases must not move whilst in motion. Black and yellow striped tape and flashing lights, as well as an audible warning, should be placed at the sites.
Flying lessons for first years. Make flying at least a 3rd year course and only students in that range can try out for Quidditch. Or Flight may be taught, provided appropriate safety measures are taken. Personal protective equipment, as well as padded flooring must be used.
Constant security breaches. Trolls, a Horcrux, a wanted criminal, a disguised Death Eater, the wardrobe in the Room of Requirement, the list goes on. Install ID-based entryways, and a sealing of all unofficial entrances to the castle.
Irresponsible Headmasters. OK, maybe only Dumbledore applies to this, but if you think about him from an occupational point of view, the guy does a terrible job. Allowing the stone to be hidden in Hogwarts, hiring Lockhart to expose him as a fraud and wasting DATDA for that year, allowing Dementors to guard Hogwarts, agreeing to host the Triwizard Tournament, using students like Harry and Draco in his conspiracies. In any other story, he'd be the villain and now I'm kind of glad he's dead. Verbally warn headmaster pending review.
The Whomping Willow. Willow must have a clearance area marked with a fence and signposted.
The Forbidden Forest. Signs listing the dangers of the forest must be placed near the entryway to warn off adventure. Forest site should not be used in detentions.
No background check on teachers. Maybe this is part of the jinx from DATDA, but there are other violations of this. Hagrid may be good with animals, but that alone doesn't qualify someone to teach zoology. And he has no PHD in zoology. Anyone with a wizard PHD in zoology would know that hippogriffs are too dangerous for first timers. And had it not been for the book's outdated morality, Harry would have been the injured one. A rigorous qualifications assessment protocol should be undertaken.
Detention in the Forbidden Forest. See 11.
Hiding the Stone. Hiding the Stone in Hogwarts was dumb, dangerous, and irresponsible. Not to mention badly done. If 11 year olds could bypass the challenges, the Stone was not well protected. Use a lock charm too powerful for alohamora. Install muzzles on fluffy. Put a light source and clearly signposted box of matches near devils snare. Clearly label all chess pieces and display the danger of participation. Broom room must have clearly labelled keys, in accordance with LOTO procedures and floors and walls should be padded. Remove troll from facility, else train to behave. Clearly label all potions in accordance with HSE/COSHH guidelines. Place 'do not break glass' sticker on mirror. Or find a better place to hide the stone.
Hosting the Triwzard Tournament. If there's one dumb, dangerous, and irresponsible thing that dwarfs the stone incident, it's the Triwizard incident. Here, someone died despite the clear cut risks that were ignored for the sake Olympic amusement. Perform risk assessments of all tasks and get consent from parents/guardians. Mitigate death by ensuring all participants have basic education in creatures involved. Or don't hold at all.
The Chamber of Secrets. Granted no one was aware of this, but you'd think after that year Hogwarts would made major modifications to it's security. But instead, things got worse and worse. See 8. Seal chamber with adequate wall, block off sink entrance with yellow and black safety tape. Clearly signpost 'no entry'.
Potions classes in dungeons with no windows or ventilation systems or spells, emergency drains, or showers. Emergency procedures should be listed here. Fire extinguishers, eye wash stations, ventilation, proper heating, and PPE such as goggles to be worn for all chemical handling. And make sure emergency drains and showers are installed. Also may want to move to another room.
No student councilors or therapists to help students with mental health problems. If they had one, Tom Riddle might have turned out better. Hire some and convert the room of requirement into a therapy office. Install guidelines for mental health help, including posters clearly pinned around school.
Placing charms on the dormitories so that the opposite sex cannot physically enter instead of getting stink bombed and making the common room smell like rotten cheese. Clearly labelled ventilation, plus warnings of entry on doors. Deactivate stairs that turn into a slide. Install wheelchair ramps in accordance with disability laws.
No sex ed. Sex ed has always been a difficult subject, but ignoring it is out of the question. Honestly it's miracle no one got someone pregnant at Hogwarts. Students should be educated in conformance with the SRE education, compulsory under the national curriculum for science.
No classes about finding jobs, keeping jobs, doing finances, and life skills. But then again, most schools don't teach this stuff. Careers advice is given by heads-of-houses throughout educational period; more frequent career consideration meetings should be considered. Hard hats not optional.