She is obviously beautiful, but she has flaws.

Literal

She [topic-は] clearly beautiful-person is [but-が] flaws [also-も] exist.

明らかに美人だが欠点もある — が marks the contrast between beauty and flaws. 欠点 (けってん, 'flaws, shortcomings') is a common Sino-Japanese compound. も adds the 'also' nuance.