When the mercenaries attack Lara's mansion, they apparently bring bungee cord ropes. Since some of the mercenaries were setting up mid-air perches, you would think that they would be using non-bouncing ropes.
The Buddhist abbot at the monastery in Cambodia extends the 'wai', a gesture of respect (both palm pressed together and held just below the chin in front of the chest), to Lara, which she returns. A Buddhist monk would never give that gesture to anyone, and certainly not to a female, nor as the initiating party. Also, while monks are greeted that way, they do not return the gesture.
Powell orders his men to fire on the leader of the Illuminati, and they shoot machine guns at him. This was a poor decision because he couldn't have been sure that any of the bullets wouldn't hit the triangle pieces. In fact, in a couple minutes, Lara destroys the Triangle by shooting it.
Just before Lara enters the auction room, the auctioneer is telling everyone there is a clock "shown to my left". When the camera goes to the expanded shot of the room, we see the clock to the audience's, not the auctioneer's, left.
In the morning after the attack on Lara's mansion when the delivery service guy comes in to deliver mail, he comes upon Lara's mansion doors open and then as he proceeds and the camera angle changes, it now appears that both doors are shut. (Note: This is because the exteriors were shot at a real mansion, but no permission was given to film inside.)
During the final action scene Lara puts her guns on the ground. In the following sequence, when she is running from the room, she has her guns holstered at her hips yet she had no opportunity to pick them up.
When Alex is counting down to get the first half of the triangle, he reaches 28 seconds. Lara then interrupts and has a conversation that lasts over 28 seconds. When Alex resumes his countdown he begins at 12 seconds again.
As the locals are trying to pull down the wall to find the first piece of the triangle, Alex West takes off his shirt and starts to pull on the rope with the rest of the gang. In the next shot he is clearly seen to the left of the screen with his shirt back on as the wall topples down, jumping up and down and shouting something.
During the shower scene near the beginning of the film, the shower head style changes between a waterfall style and a standard spray type. You can see in some of the cuts that the waterfall does not have any spray coming off it but in other cuts her head is surrounded by spray from a standard shower head.
It is stated at the start that there will be an alignment of all 9 planets, resulting in a full solar eclipse. The 9 planets never align completely, and never will due to the orientation and tilt of their orbits. The closest was all of them in the same part of the sky in 949AD, and will again happen on 6th May 2492.
When Lara defeats Powell, she kills him by delivering a chop to his throat. Realistically speaking such a move would have crushed Powell's trachea and caused him to gasp for air until he suffocated. His death would have taken several minutes yet, he falls dead instantly as soon as Lara delivers the final blow.
Upon entering the tomb with the model of the solar system, all the characters shed their jackets and, in Lara's case, capes. However, they are still inside of an ice cave in the Siberian mountains. Surely they would all be freezing cold.
There is no way that the pillar Lara rides to burst the glass urn in the first tomb would still be swinging hard/far enough for it to do any damage to the Vishnu statue that comes to life, also even if it was, the pillar can not possibly be so light that someone of Angelina Jolie/Lara Croft's size could alter it's path so dramatically.
Lord Richard Croft states that the two halves of the triangle were taken from the city in the crater and hidden at opposite ends of the earth. Despite this the second half is found in the city itself in Siberia, and the first in Cambodia, on the same continent.
Lara's whole goal in the film is to destroy the triangle so the Illuminati can't use it's evil power, however, after successfully getting the first half at the first tomb, she spends the entire third act trying to acquire the second half in order to destroy them both. The problem is that she has one piece already and one half can not work without joining it with the other, so why doesn't she just destroy the one she has, rendering the second piece useless?
At the end of the film, Lara goes back in time to save Alex, but when she does this, the Triangle is floating a few feet away. The problem is that she has returned to a time before they put the triangle together, so why is it there?
Both tombs contain an obvious error. The first is (judging by how far Lara falls) located deep underground, and the second is located in a cave in the Siberian mountains, however each is amazingly well lit, considering neither should have a source of sunlight.
Lara finds the clock at night. She then goes to Bryce's trailer, where it is pitch black, and mentions that it is five in the morning. One would assume that she immediately went to Bryce after finding the clock, however Lara then tells him that she "found it last night". So Lara waiting at least 5 hours before consulting with Bryce? Furthermore, there is light flooding through all of the mansion's windows during this scene. Lara then leaves to go to the auction house and it it clearly the middle of the day. How long did it take Lara to show Bryce the clock considering it was completely dark out when she woke him up to come look at it?
During the attack on her mansion, Lara picks up a commando between her legs, and with the help of her bungee cord, throws him into two other commandos. When they fall, you can clearly see that the HK G36's they're carrying are rubber, because one of the barrels bends as it hits the ground and stays at an awkward angle.
In the opening fight scene, Lara slams her back against a sarcophagus in order to pause to reload her guns. The sarcophagus gives forward and shakes in reaction to Lara's back, revealing it to be made of rubber or some soft material in order to not hurt Angelina Jolie's back.
Before the attack in Lara's mansion she receives a letter from her father. Before she opens the letter she looks at it and appears to be reading something on the front of the paper, however she then flips the paper over and the paper can be clearly seen as blank.
When Manfred Powell is laying on the tomb floor at the end of
the movie, with a knife stuck in his chest, he is laying down using a small step as a "pillow" and in the next shot the step is up under the small of his back. The next shot he is using it as a "pillow" again.
When Lara returns back in time and intercepts the knife being thrown at Alex, time is frozen while she twists the knife around redirecting it towards Powell; yet the orrery in the background continues to rotate.