Executive Meddling: The movie got hit hard by this. For starters, the script got sent back because the studio was afraid of backlash over the removal of Harry Mason. This is why the film frequently cuts back to Chris in the real world, which was one of the most common criticisms among fans.
There were also some key scenes that were cut for time, among other things, this included more Lying Figures and Alessa actually showing some supernatural abilities when she was a child.
Konami literally murdered the series outright in 2015 when they cancelled Silent Hills because of... reasons. Presumably Konami had reasons for cancelling the most-anticipated installment of one of their most long-running and highly-regarded series, the first one in 3 years, but whatever they were, they didn't feel like sharing what exactly they were. In the 3+ years since then there's been a pachinko machine and... uh...
Shrug of God: The creators are frustratingly coy about which of the endings are canonical. A few of the additional releasesonly available in Japan do shine some light on things, but real answers are as rare as ampoules. However, later events and exposition in the series' chronology dictate that Silent Hill 1, 3, and Origins had good endings, and also heavily imply that Silent Hill 2's true ending was "In Water".
To many, though, this simply makes the games scarier since it allows for more speculation about the series. Because pretty much everything is symbolic of something and there is no true answer to many of these questions, it makes the nature of the town that much more unsettling.
A case of "What Couldn't Have Been": Guy Cihi was originally just at the auditions for Silent Hill 2 because his daughter was interested in a role. But Cihi had some background with acting in high school and college, and became interested in auditioning himself. Ultimately, he landed the role of James Sunderland, the game's protagonist!
Meanwhile, Cihi's daughter auditioned unsuccessfully for the role of Laura. Had she gotten it, that would add a whole new subtext to the game's 'Leave' ending.
Before Homecoming, one of the original ideas for the series' seventh-gen debut came from Climax Studios (makers of Origins and later Shattered Memories), which would have followed a priest from El Paso named Hector Santos who does battle with the Order in the small Arizona town of Coyote Flats, where they had relocated to some time after the events of the first game. The Otherworld would've involved traversing multiple versions of the town from various time periods going back to the 17th century, indicating that Alessa's influence had spread far beyond Silent Hill and had followed the cult west. After Konami declined to have it as a Silent Hill game, Climax tried to retool it into a Divorced Installment called Broken Covenant, but they never found a publisher to support it.
Before Shattered Memories was released on the Wii, there was another proposed title called ''Cold Heart'' which would have followed a college student named Jessica Chambers struggling with nightmares and insomnia. It is believed the reason it never got past being a pitch is the development team was expecting too much from the Wii console's capabilities and what it can and cannot handle. Some of the concepts from the pitch were later used in Shattered Memories.
The official canon for Silent Hill is that it is located in Maine. Not surprising, given that it's heavily based on the works of lifelong Mainer Stephen King (raised in Durham, and currently living in Portland), with his books and their film adaptations given numerous Shout Outs. Although its precise location was ambiguous for a long time, several hints throughout the series implied Silent Hill to be in Maine, and many fan theories placed it (as well as other towns like South Ashfield and Shepherd's Glen) in Maine, or at least in New England.
The Japanese publication The Book of Lost Memories, as well as the instruction manuals for the original game, Origins, and Homecoming, have all stated more generically that the town is located in New England. The Book of Lost Memories' timeline also makes special mention of the founding of the state of Maine.
The Gillespie House is based on the real life Olson House, which is located in Cushing, Maine.
In Silent Hill: The Novel, Harry feels he should have been enjoying the "Maine wilderness" with his daughter, rather than searching for her.
Further information can be found in the third game. After Harry Mason left Silent Hill, he and Heather Mason moved to Portland, which could indicate the one in Maine or the one in Oregon.
Inside the liner notes for the Japanese release of Silent Hill 4: The Room's soundtrack, an address is given for Heaven's Night that would have placed it in Maine. The state abbreviation for Maine is "ME".
In Double Under Dusk, a Silent Hill comic by Hiroyuki Owaku (scenario writer of the first games in the series), Silent Hill is placed in Maine. The two protagonists, Brian and Lindsay, are from Augusta and Orono, respectively.
In Homecoming, there is a book shelf which contains information about mining towns of New England in Shepherd's Glen Town Hall.
In Downpour, the prison transfer bus carrying Murphy Pendleton is seen bearing a Maine license plate, and a road sign bears the Interstate 95 logo, a highway that runs through and ends in Maine. Likewise, when Murphy is about to get on the bus, Anne Cunningham stops him. Her clipboard shows "Maine State Board of Corrections" on it. Interestingly, Stephen King's The Shawshank Redemption is cited as an inspiration for Downpour, and its story is also set in Maine.
In the movie, Silent Hill is canonically located in West Virginia. Beyond that, it is very obviously modeled after Centralia, Pennsylvania, where a long-burning coal fire has caused most of the residents to be relocated elsewhere.
Shattered Memories uses the 49504 zip code of Grand Rapids, Michigan. And yet there's a street-sign right near Harry's car at the start that says Buffalo and Rochester (both Western NY cities) are less than 70 miles from where the town is, indicating a location in upstate New York or even Ontario. Then again, the sign is laying on the ground in a junkyard.
The receipt that kicks off the Kaufmann sidequest in the first game mentions a sales tax of either 6.25% or 6.75%. Not very helpful by itself perhaps, but in conjunction with other evidence, it might tell us something.
Many of the cars in Silent Hill 2 and 3 have (admittedly blurry) license plates that resemble Illinois plates.
Creator Breakdown: Implied to have happened with Jodelle Ferland for her portrayal as DarkAlessa, albeit not permanently or fatally. It is reported that the writer, Roger Avary, apologized to Jodelle's parents for any mental trauma she may have incurred from playing the role.
Doing It for the Art: Every monster in the movie is a person inside a suit, with some CGI effects added afterwards. Unfortunately many people ended up thinking them as shoddy CGI, due to their unnatural movements, which in fact are the result of the skill of their actors, and unusual camera techniques in shooting them; for example, the bubble-head nurses were choreographed doing their movements backwards, and the film was then reversed for the effect.
Executive Meddling: A fairly bizarre example. Sean Bean was cast as Christopher because the studio felt that they needed an allusion to Harry Mason in the film, hence why his scenes often seem so disconnected to the main story and rarely overlap. Ironically, had they simply kept Harry as the main protagonist and not changed him into Rose, this wouldn't have even been a problem.
Throw It In!: Colin flicking his tongue in a disturbingly sexual manner wasn't in the script. His actor did it as a joke in one take, but director Christophe Gans liked how it looked and kept it in.
Uncanny Valley: Invoked. The nurses' unsettling movements were achieved by having the dancers/actors perform all the on-screen motions backwards and then playing the footage in reverse.
What Could Have Been: Several scenes were trimmed or rewritten due to time or budgetary constraints;
A more elaborate setpiece was planned for the initial meeting with Anna, with her being attacked by an injured armless creature and being saved by Rose and Cybil. Due to exhaustion, actor and choreographer Roberto Campanella was sent home early, and the scene was rewritten to the simpler variation seen in the final film.
The climax in the church originally involved six Pyramid Heads, each with a different weapon, killing the cultists en masse in reference to The Divine Comedy, but due to budget and time constraints, the scene was rewritten to the one seen in the film, which reportedly was inspired by Urotsukidoji: Legend of the Overfiend.