Other mistake: When we see the body of Liz Stride after her throat has been cut, the blood is bright pink. This may be due to the light shining on it, but it's still pink. (Surely by then, the blood would have turned brown after mixing with the oxygen?).
Other mistake: When The Ripper is with Liz Stride, she drops her grapes in a puddle. When she kneels down to pick them up, she sees him in the reflection holding a knife and standing behind her and to her right. When the shot changes, he is directly behind her, and thus his reflection would not have been visible to her.
Other mistake: Towards the end of the film when Abberline is kidnapped, you see the carriage he is in cross a bridge over the Thames. In the distance (beneath one of the arches) you can see a tall illuminated building.
Answer: His eyes are not just darker, his entire eyes are completely black. This was done by CGI effects to show that the murderous Ripper side to Gull's persona is taking over and is in control.
Twotall