Thanks to Sarah for collecting these from Lostpedia.
When the alarm clock goes off in the opening scene, the alarm itself isn't actually set. The alarm is set on the left-side of the clock and is set to 12:00.
Pierre Chang can be seen wearing a Swan logo despite making the orientation video for the Arrow. After Desmond recalls his "memory" he goes above deck to begin pulling up the anchor, but in actuality the chain is going in the reverse direction, lowering the anchor.
Goldie parachuted from the Beechcraft into the trees near the crash site, but we see the plane fly very low and crash quickly, leaving him no time to have done this. This also does not match Locke's Vision in "Deus Ex Machina", where he sees the plane crashing directly down into the trees from the sky.
The DHARMA worker wearing the Fern shirt is portrayed by a different actress than the one seen in (Lost: The Complete Third Season (DVD)).
Sun's passport is displayed in Adobe Photoshop, probably filmed soon after it was created by a graphic artist for the show.
When the witness takes a picture of Hurley with the gun, the man Sayid threw over the railing is shown in a different position than the one in which he landed.
The rip in Desmond's HAZMAT suit is now on the left leg, as opposed to when it was on Kelvin's right leg in "Live Together, Die Alone".
Source: Lostpedia