The younger Estefania has two rather prominent moles on her neck and below her collar-bone. The older Estefania has none.
Young Estefania has a dark scar on her upper left cheek near her eye; no attempt to reproduce this scar appears on Estefania once she is older.
(at around 1h 14 mins) The gun that João gives to Jorge is different from the one he pulled out in the classroom just moments earlier.
When Jeremy Irons is in a boat in the river with bridge Salazar (at time) in the background, you can see a train going trough the bridge. At that time Salazar bridge doesn't had railroad. Brigde was upgraded and installed a railroad in the lower deck in 1999.
When Raimund is on the Bern Train Station, he is thinking whether he goes on board or not. The train starts to move and the doors are still open, which nowadays it would be impossible in trains of that dimension for security reasons. Although the error was needed to give more tension to the scene, it is still a thing that would never occur nowadays.
The chess set has the knights and bishops reversed.
Raimund is watching the pharmacy from outside and Older Jorge is smoking inside a pharmacy attending customers. The law in Portugal strictly prohibits smoking in any building since 2008. But in pharmacies, long before that it was almost unthinkable to see pharmaceuticals to smoke while attending customers. Although it gives impact to the character of Older Jorge, it is almost impossible to see that in 21st century in Portugal.
when his sister chokes whilst Amadeu is studying for finals, he uses the Heimlich maneuver unsuccessfully.
The Heimlich maneuver was invented in 1974 (the year in which Amadeu dies and the Portugese revolution occurs) after Amadeu has qualified.
When Raimund (Irons) comes to the hotel (my timer shows 51 minute of the movie length), he takes the keys, and then in the room he opens the closet door, and we see the film crew members (the two contours) reflecting in mirror of that door.