1) Jason Robards (give yourself a pat on the back if you know who he is) and Mick Jagger were the original two leads -
Unfortunately Robards came down with severe dysentery after FORTY PERCENT of the film was completed. Jagger could not wait the seven to nine months required for Robards to convalesce and quit the project as well. Herzog had to scrape everything he had shot so far and press the reboot button with a new lead, Klaus Kinski (give yourself another pat on the back if you know who he is).
Frankly, Robards/Jagger kinda sucked. In my opinion, their departure was kinda fortuitous since it brought Kinski into the picture.
2) Klaus Kinski is a one-man walking disaster (In Herzog's words, Brando is kindergarten compared to Kinski). Here is Kinski having an argument with Walter Saxer, the producer -
Btw, this was considered a minor tantrum (he didn't hit anyone or walk off the set). One of the greatest actors of his generation, but probably the most volatile as well. A physical entity made up of equal parts insanity and melancholy (one cannot stare at his face without feeling just a little bit sad), he was a constant menace and troublemaker to everyone he came into contact with (yet strangely enough, was in popular demand).
3) There was a border war going on nearby between Ecuador and Peru. One day, soldiers came over and held everyone at gunpoint. They forced everyone off the set before burning everything. Herzog had to start from scratch. AGAIN.
4) The Brazilian engineer who designed the initial pulley system to drag the steamship over the patch of rainforest quit, saying Herzog was crazy and 70% of the natives would die. Herzog went ahead anyway. The pulley gave way (fortunately, no one was hurt). It didn't help that the bulldozer kept breaking down and the spare parts had to be flown in from America.
After hiring a brand new engineering team, he continued. But that was after many months of begging for new investors (the money ran out).
5) The filming, originally timed to coincide with the rainy season, had to be pushed back many months due to the numerous delays. By the time filming began, the Amazon was experiencing its driest patch of weather in decades. Unable to navigate the knee-deep water, the steamships were stuck in place for seven months. Everyone went home and came back seven months later.