After Tom is beaten by Flashman wearing the knuckle-duster, he is shown with two deep gashes on his face. In the next scene, his face is clear of damage, but in the next appearance, there is evidence of healing wounds.
When Tom Brown and East encounter Flashman the school bully while carrying water, at one point East is in front of Brown, the next view East is behind Brown.
In the time period the movie was set, modern orthodontic braces had not been invented and therefore weren't used, but one boy is clearly seen wearing them during the rugby scene.
The film features several shots of Rugby School's Chapel, which wasn't built until 1875 - over thirty years after Thomas Arnold's death.
While the boys are playing rugby, in a completed tackle the boys stand up to cheer. In the far background you can see clearly a white van.