When discussing the super weapon with Burke, Turnbull claims Eli Whitney started the Industrial Revolution with the invention of the cotton gin. While that was an important invention of the era, the Industrial Revolution actually started in the United Kingdom.
As Turnbull is talking to Burke about Eli Whitney, Michael Fassbender's lips can be seen moving as John Malkovich recites his lines.
The flag flown by Turnbull's ship (with thirteen red/white bars and the blue area containing two concentric circles of stars +4 stars in the corners [35 total]) is the US CAVALRY Guidon, NOT the US Flag of Grant's era (which had 37 stars in 5 rows, 8/7/7/7/8 )
Even though the flag came into existence at the beginning of the civil war, it was reserved solely for use by the Cavalry ... all SHIPS were required to show either the US flag (Union and post war), or the Confederate Navy flag.
In the still photograph of Lilah (Megan Fox) where a slip of paper is tucked under her corset, you can see her tattoo through the fabric which reads "Brian".
The Washington Monument is shown as almost complete. In 1876 the Monument was still only one third complete and construction had been stopped since 1858. Addition construction was authorized during the Centenial but actual construction did not resume until 1879.
When Turnbull is explaining the origin of the "super weapon" to Burke, he attributes it to Eli Whitney, Senior. In fact, it was Eli Whitney, Junior he is describing.
When the liquid is poured on Jonah's chest the poultice is not there but is there again in the next shot.
The train locomotive has a Vanderbilt-style tender (fuel and water car), a design not invented until 1901. Tenders at this time were of a simple, box-like design.
In the Train Hijack scene at the beginning the wooden crates are marked U.S Carbine 30 Cal. Krag-Jorgenson. Krags were not adopted by the U.S. Army until 1894.
When Lieutenant Grass first meets Jonah Hex after shaving, his moustache on his right side is crooked, showing it's a prosthetic. It is corrected in the next shot.
Megan Fox's outfits are clearly inappropriate for the era in which the film is set. Women, even prostitutes would never dream of walking around outside showing more skin than was absolutely necessary.
It is unlikely that a poor man/criminal like Burke would have been able to afford the number and detail of tattoos that he is shown having. Tattoos were extremely expensive until electric needles were available following WWI. Until that time tattooing was almost exclusively the province of the wealthy, mariners and some members of the military.
In the shot at the large lake toward the beginning of the movie you can see what looks like a white buoy floating in the background. White plastic floating buoys did not exist in the time of the movie.
After Jonah uses the guns mounted on his saddle they suddenly have the blankets wrapped around them again.
During the final fight scene Jonah Hex fires a gun into a box of dynamite and lights a fuse on one of the sticks. For safety dynamite and fuses/blasting caps are keep separate until just before they are set.
The Gatling gun setup that Jonah Hex uses in the beginning exhibited no actual recoil as his horse is not shown to be stepping back or bucking when it fires. Additionally, the Gatling gun fires far too many shots as Gatling guns were feed from a stick magazine mounted in the top and were limited to 50 rounds per magazine.