"Let's get straight to the truth. Weren't you at the bakery at midnight?"

The detective is using a negative question to confirm something he already believes is true. For the pronoun "you," the correct past tense form of the verb to be is were, making the negative question Weren't you.

"And isn't it true that your fingerprints were found on the last chocolate donut?"

We use isn't it to ask for agreement or confirmation about a current fact. Since the phrase is "it is true," the negative question form is isn't it true.