They're going through a rough patch right now because of percentages of $$$$. The new head of WB is trying to solve the conflict but it's not currently working.
Keep in mind that Legendary isn't just a finance company. Thomas Tull is not just a business man, but also the creative type, which is somewhat rare in Hollywood. That's why it's a shame Legendary may be leaving WB. Which means WB is on their own with their DC films (MoS 2, Justice League) and may lose the distribution rights to future films like Godzilla 2 or Pac Rim 2.
That's why WB renewed contracts with other production companies like Alcon, etc because they know they might lose Legendary. Also, keep in mind, Legendary owns 'Warcraft' so that may not be a WB partnership. That's why WB is pushing for 'Dungeons and Dragons' on their own to level the playing field.
But in the end, a movie like Pac Rim could NOT exist without Legendary. They fully (or mostly) financed the film by themselves if I'm not mistaken.