Danny dropped the box of ammo on the stairs and some of it spilt onto the floor. He picked up some, and kept running up. When Spider's accomplice sees the box, the ammo is in a different pattern and there appears to be less of it.
During Mac's flashback, he is in front of his bike as he tries to flag down the first car. As the car passes, and he turns around, the bike is further in front of him.
MacGyver adds a cleaner to phenolphthalein and then uses the mixture to make a trail of fake blood. Phenolphthalein turns pink when an acid is added. It does not turn red enough to appear to be blood, and it is watery. When he makes hand-prints of blood on the wall, they are faint at the time, but much more blood-like and deep red when shown later. This level of red cannot be reached by phenolphthalein.
The stunt double for MacGyver is noticeable when the shelving is pushed over onto him.