The actress told TV Guide that she remains "professional" even if she dislikes an aspect of the medical drama's scripts.
"It's always a challenging balance, but it's always my goal to do things that make the character grow and seem more mature," she said. "At the same time, they're always going to write certain behaviours that I only have so much control over."
Pompeo pointed to her character Meredith turning down a job opportunity at Harvard as a plot point that she had trouble with, calling the doctor's decision "a bit of a stretch".
"That's a difficult thing to believe when I'm playing it, but I'm just a paid employee who has to do what they say," she suggested. "We have a boss like everybody else. You may not always agree with it but you still have to be professional and do the best you can."
True Blood actress Adina Porter recently signed up for a guest role on the new season of Grey's Anatomy.
The show's ninth run premieres on ABC in the US on Thursday, September 27 at 9/8c. In the UK, Grey's Anatomy airs on Sky Living.
> Grey's Anatomy ninth season to feature flashbacks, says Kevin McKidd
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Watch a promo for the return of Grey's Anatomy below: