When Maggie and the kids arrive in Springwood, the graffiti on the van has changed from the earlier scene when they left the youth center.
(at around 44 mins) When Freddy is playing the video game he alternates between having one foot up on the edge of the table and both legs crossed in the middle of the table between shots.
When Spencer, Tracy, and Carlos enter the empty house in Springwood, the lights in the front door window are on. But when the door is open, you can see that it is pitch black inside. When the door is shut again, the lights are on again.
(at around 37 mins) When Freddy is dropping the needles from above, we see Carlos reaching up with two arms, but in the close-up, he's bending down covering his ears.
(at around 1h 17 mins) When Maggie wakes up from her last dream, the 3-D glasses can be seen lying on her stomach for a second before she moves.
(at around 28 mins) When John Doe and Maggie go to the school, Maggie finds a scrap book filled with articles related to Fred Krueger. In a close up of the book, an article is titled "Krueger Sought: Boy, 7, Missing" but the text that follows discusses baseball (Yankees, Kansas City, and the Mets) on the left side and military action in Vietnam on the right side.
(at around 37 mins) During the Carlos Blackboard scene, you can clearly see that the glove knives have plastic or rubber tips on them.
(at around 1h 13 mins) When young Freddy is getting ready to smash the gerbil, we see him sneak it off the table as he puts it down.
(at around 1h 5 mins) When Freddy appears to Tracey as her father and he turns his glove into a buzz saw, the wires for the fake Freddy arm are visible. Also you can see Robert Englund's right arm sticking down, in front.
(at around 51 mins) When Freddy is descending from inside the parachute that "John Doe" is on, the wire that's supporting him is clearly visible.
(at around 12 mins) Just after Tracy is finished hitting the punching bag she says to Carlos "you ain't gettin' none", but it is clear that her mouth does not move.
(at around 59 mins) During Maggie's flashback/dream sequence, the cameraman's shadow is seen during the POV shot of the young Maggie running through the yard.
(at around 1h 7 mins) When Freddy is talking to Doc and cutting off his fingers, a white tube held between middle and ring fingers spurting green liquid is visible (both from Freddy's perspective and when the shot faces Freddy).
The harness that picks Spencer up is visible on his chest in the close-up of him bouncing across the living room.
(at around 47 mins) When Spencer is almost falling off the edge of the top stair (and the ledge in Freddy's video game), in his shadow you can clearly see the cord attached to his harness keeping him up.
The film spends the first half convincing the audience and characters that John Doe (a teenager) is Freddy's son before revealing that Maggie (played by 29/30 year old Lisa Zane) is his daughter. The film takes place in 2001, meaning Freddy (died in 1968) would've died around 20 years before John Doe was born and, based on her age in flashbacks, Maggie would've needed to be pushing 40 to be his daughter.
During Spencer's dream, Freddy says "What are you on? Looks like a frying pan and some eggs to me". Johnny Depp's character only had/cracked a single egg.