Muldaur got paid more than she was. Also, Muldaur was going to appear in the opening credits behind Stewart and Frakes. Sirtis opposed to that.
Unlikely. Billing in unionized film and TV is negotiated and part of the contract. The order of the credits was determined in season 1, and the way it worked was Stewart and Frakes first, and the remaining regular cast in alphabetical order based on last name. As a new actor coming into established billing Muldaur would either have been inserted as the last actor credited (as was the case when Jonathan Harris was added to Lost In Space) or—if the contract wasn't specific about the number of credits in the opening— inserted into the opening credits alphabetically (Burton, Dorn, Muldaur, Sirtis, Spiner, Wheaton). Instead, she chose to have a "Special Guest Star" credit in the credits at the top of the Act One.