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Were. The subject of this sentence is plural (we) so the verb should be a plural verb, also the other verb (knew) is past tense.
The past plural form of are is were. -- We knew we were in trouble.
Totally i knew you were trouble by Taylor swift !
The song " I knew you were trouble" by Taylor Alison Swift is Harold Edward Styles. (Harry Styles)
Knew is past tense so are should be in past tense too. Past tense of are is were.
We knew we were in trouble
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