There is only one scene involving an animatronic lion. All the other shots were used using two real life lions named Bongo and Caeser. The same lions also appeared in the film George of the Jungle (1997).
After the lions were killed, their skins were used as rugs by Col. Patterson. They were later sold to the Field Museum of Natural History in Chicago, who had them stuffed and placed on display. Because they were originally used as rugs with resulting deterioration of the hides, the lions are much smaller than they originally were.
The real John Patterson is credited with killing both lions on his own, and Val Kilmer's character John Patterson does indeed kill two lions on his own in the movie. The first is indeed a mane-less lion (as a Tzavo male lion might be, though not considered part of the Ghost/Darkness pair in the film) killed by Patterson on his first night in the encampment. The second is the second lion of the "Ghost/Darkness" pair. Patterson also wounded the first lion of the pair with a handgun and then (the fictional) Remington finished the lion off.
The Lions of Tsavo were maneless, perhaps due to environmental variables, although maneless lions are not unique to Tsavo. Their taste for man may have been due to an outbreak of Rinderpest at the time, which may have depleted their normal prey. The legend surrounding this event is almost entirely based on the books written by Patterson which became run-away best sellers for their day, and made Patterson a good bit of money. It is possible, if not probable, the count of 140 deaths may have been trumped up a bit. Patterson certainly set himself up as the hero of the story, which certainly fit in with the Western notion of the "great white hunter" of the period. It is known that he killed both lions (both nearly nine feet long), and that they did indeed kill and eat humans. It is also possible that they did this because they may not have been able to kill and eat their normal prey as the jaws of the two show some sign of unusual dental disease. They now reside in the permanent collection of the Field Museum of Chicago, but the government of Kenya is moving to try to obtain the pair.
The rifle used by Val Kilmer is a "Lee Speed" sporter, most likely in .303 caliber. The movie rifle is historically correct and most likely came from a South African movie prop supply house. BSA made these rifles from 1892 until at least the 1930s in .303, 7mm, and 8mm. BSA offered several different versions and options on these rifles. The term "Lee Speed" was used for commercial rifles. These rifles were mostly manufactured by the BSA Company, who also made Gov't rifles (Lee-Enfield Mk1 NoIII being the most common) and had the machinery in place to make sporting versions.
Theatrical trailer shows two alternate scenes; Alternate take and angle of the scene where Samuel says "They are not lions, they are the ghost and the darkness" and alternate close up angles of Patterson and Remington during the scene where they are preparing trap for lions and are talking about how many people did the lions killed. Making of documentary shows following deleted scenes; Samuel saying "If we stay, we will all die" (it looks like this was part of his same alternate scene shown in trailer), Samuel and Patterson standing on the bridge and looking at jungle when Samuel asks Patterson "Do you know what Tsavo means?" when Patterson says no Samuel says "The place of slaughter", alternate/additional narration by Samuel about the story of two lions where he says "This is the most famous true story of Africa. But even know, when children ask about it, you do not tell them at night", extended dialogue in scene where Remington and Patterson first meet and Remington says one extra line "Stay out of my way".
William Goldman first heard about the story when travelling in Africa in 1984, and thought it would make a good script. In 1989 he pitched the story to Paramount as a cross between Lawrence of Arabia (1962) and Jaws (1975), and they commissioned him to write a screenplay which he delivered in 1990.
Director Stephen Hopkins said in 1999 interview with SFX magazine how making of The Ghost and the Darkness was his worst experience as a filmmaker, "a true nightmare". Michael Douglas, who was producing the film, decided at last minute to play the Remington character. But even before filming began the working relationship between Douglas and Hopkins was very tense. Douglas even went and had the movie completely re-cut in post production removing 45 minutes of scenes in order for him to have more screen time. This also explains story parts that go nowhere and plot holes that the movie has. Like for example, a part where the story jumps from having only few people killed by lions only for characters in next scenes mentioning how the number of people dead is much bigger. Hopkins expressed disappointment with the final cut of the film.
In original drafts Remington was called Redbeard, and William Goldman says his purpose in the story was to create an imposing character who could be killed by the lions and make Patterson seem more brave.
Patterson was not an engineer; he didn't design or draw any plans for the bridge. He was commissioned by the Uganda Railway committee in London to oversee the construction of a railway bridge over the Tsavo River. (biography quote). His son, Bryan, was born in 1909, hence, his wife's arrival, holding son high, etc. is just screenwriter's addition to the film. The bridge was finished in February of 1899.
In early drafts of the script, Remington was originally going to be an enigmatic figure but when Michael Douglas chose to play him, the character's role was expanded and was given a history. In William Goldman's book Which Lie Did I Tell?, the screenwriter argues that Douglas' decision ruined the mystery of the character, making him a wimp and a loser.