When Duncan fights the Guardian near the end of the film, his wife Anna is standing in the "Source," at the top of a set of stairs at one end of the pit. After the Guardian stabs Duncan, he is standing between the two of them, with Duncan and Anna at opposite ends of the pit. Watch the closeup of Duncan just before the Guardian begins to spin a tornado by waving his sword; you can clearly see Anna standing at the top of the stairs behind him, even though she's supposed to be behind the Guardian.
In the scene at the monastery, Duncan and Joe breaks through the monastery door with Joe's jeep. A few minutes later, as the Guardian arrives, Reggie goes out to fight him, and the monastery door is unharmed.
The Elder says that as the immortals get closer to the Source, they will grow weaker and lose their immortality. However, when Duncan reaches the Source, he suddenly gains super-speed. This is even dumber because the Guardian flat-out states that the Source is filling him with energy.
The Source prevents the immortals from being able to sense other immortals. Late in the movie, the immortals say that they can sense the Guardian, even though earlier, they could not sense him at a geographic point farther away from the Source.
If Jupiter and Saturn were closer to the Earth than Earth's moon (as is shown late in the movie), the entire solar system would be destroyed due to gravitational imbalance--let alone Earth being destroyed.
How did this world descend into chaos in what couldn't possibly be more than a 5-year time difference between this movie and the previous one? Joe Dawson is the same age as he is in the Highlander TV series, so there is no way takes place a long way into the future.
Methos and Giovanni clearly know who the Guardian is when they are talking via their computers. However, when they all go to speak to the Elder, they seem to have no idea who he is as the Elder tells the story of his becoming the Guardian of the Source.