Alias

Phase One - S2-E13

Plot hole: In 'Phase One' Sydney tells Will during the day to "Get Francie and get out of town" because she realises there's someone after her. Later that night Francie is shot at her restaurant and replaced by Allison (the clone), but Will was supposed to have taken her away already. There's no question of him not finding her - the restaurant would be the first place he'd look for her.

Shay

Second Double - S2-E21

Plot hole: When Sydney is visiting Will in jail, she says that the CIA changed all the passwords. However in a later scene, Weiss asks will for his password, and Will says that it's "Sydney." If the passwords were changed, wouldn't Will's have been changed too?

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