The Cliffnotes version:
** John Rhys Davies' controversial death in "Exodus" (via having his brains sucked out, being shot and then left to die on an exploding planet) was caused by behind-the-scenes issues. Rhys-Davies allegedly insulted then-producer David Peckinpah (while drunk) at a party hosted by Fox brass when the series first began. Later on, when Peckinpah was promoted and gained control of the series, he used this leverage to convince the network to fire the actor (via the release of his episode contract), and gave him the fate he endured in the episode.
** Kari Wuhrer's presence on the show in the third season caused massive friction between herself and Sabrina Lloyd. During a script-reading, Wuhrer made snide comments about Lloyd's engagement to one of the crew members, which caused Lloyd to break down and cry in her trailer, thus holding up production for hours. David Peckinpah (who first approached Wuhrer to star on the show) used this incident to spread lies about Sabrina costing the network money, and eventually told her point-blank that he would support Wuhrer and not her (prompting her to leave the series). Even worse, Peckinpah later twisted the knife by condemning Lloyd's character, Wade, to being raped in a Kromagg breeding camp - the only reason it didn't come off looking even worse is because the production staff led a revolt to change the plot to something more meaningful (via the introduction of the Humaggs).