When Joel, Tess & Ellie are eating (about 14 mins in), you see Ellie's sandwich have fewer bites out it from one shot to the next.
When Ibu Ratna is picked up in the restaurant, she is wearing glasses. She's also wearing glasses when she gets to the lab (though she takes them off to look in the microscope) and when talking, after leaving the quarantine room.
However, when she's in the hazmat suit, she is not wearing glasses.
However, when she's in the hazmat suit, she is not wearing glasses.
When Joel, Tess, and Ellie travel through the flooded hotel lobby, their pants get wet (up to knee high). As they climb up the hotel, their pants are longer wet.
The bites taken on Ellie's sandwich change sides between shots.
The grenades wouldn't detonate from the fire.
When Christine Hakim is collected from a restaurant in 'Jakarta', the set design depicts Bali. Not only do the number plates of the vehicles in the traffic begin with DK (Denpasar), but there is also a clear shot of a sign for Kuta Square, which is close to the beach near the Hard Rock in Kuta, Bali.
The liquid that Tess spills on the floor is diesel. Diesel isn't flammable at a normal environmental temperature. So when Tess dropped her flaming lighter, the fuel on the floor would not have ignited and if the fuel did ignite it still wouldn't have been hot enough to make the grenades detonate.
After 20 years mother nature has taken her toll on the landscape and buildings in Boston. YET, the flags on top of the museum are in great shape despite 20 years of wear and tear (exposure to sunlight, rain, wind, ...). Rather, after 20 years of weathering, the flags should have been shredded with very little still attached to the flagpole line. Further, the flagpole line itself would have deteriorated if not broken, causing what little was left of the flag to be carried away in any succeeding gale.
Joel, Ellie,and Tess go to the Massachusetts State House, recognizable by its golden dome. However, Marlene had told them that the team they were meeting would be set up at the Old State House, a colonial Era building near Quincy Market.
Joel, Ellie, and Tess look west across Quincy Market, with Fanueil Hall and Boston City Hall visible in the background. However, this would mean that they came from the east, which consists of Boston Harbor, not the cityscape they were shown traveling through.
The protagonists are shown approaching the front of the Massachusetts State House along a broad avenue with a clear view of the State House. In reality, the State House fronts onto Boston Common, a large open park. None of the streets on the opposite side of the park point directly at the State House.
The path that Joel, Ellie and Tess take makes no sense in regards to Boston geography. They camped for the night in the Financial District (based on the plethora of skyscrapers and Tess' comment that they were a ten minute walk from the State House). They then apparently detour to some place with an elevated highway, before heading to the eastern end of Quincy Market, which is in the opposite direction from the State House, before returning south to the Theater District for the final approach to the State House.