The position of the pendulum blade changes between shots. In long shots it's above McGyver's legs, but in close-ups it's above his chest.
When MacGyver is flying through the air in the box, the clouds in the background are standing still.
The helicopter seen at the beginning is a Eurocopter/Aerospatiale AS350 Ecureuil (AStar) which has a 3 bladed main rotor, but the sound heard is that of a 2 bladed helicopter such as a Bell 206 JetRanger.
At the end, Zoe and MacGyver do absolutely nothing to prevent von Leer's henchman from grabbing Mac and tying him down under the sickle pendulum. Mac not only didn't put up a fight but he just quiescently laid while he was slowly shackled. And Zoe did nothing (by threatening to crush the artifacts) to get them to stop.