Plot hole: The Nomex survival suit that Bruce gets from Lucius Fox in Batman Begins is bulletproof, knife proof, and can stop anything but a straight-shot, per Fox. All Bruce did was spray paint over it to make the batsuit. But in the beginning of The Dark Knight, Batman gets mauled by a dog which chews through the suit and cuts Bruce's arm, causing him to need stitches.
Suggested correction: The suit still has seams, through which the dogs can bite.
The suit he was wearing is knife proof, meaning there's aren't suppose to be any "seams" for a dog to bite through. It was the later suit he requested that would be vulnerable to knife attacks.
Lucius told Bruce in Batman Begins that it would stop a knife, he didn't say it was knife proof. This was likely in reference to protecting vital organs from stab attacks, etc, not the weakest areas in his armor from dog bites. There was always going to be flexibility, protection, and weight consideration trade-offs for optimization purposes with any armor he wore, not just his 2nd.