Every time a market has been taken down it's been due to OPSEC failure and other information leaks (e.g. Silk Road captcha IP leak, DPR's advertising of market being linked to his personal email address). AlphaBay Which got taken down first in this operation was due to a personal email being included in the header of the welcome email sent out to new users 3 years ago [1]
[1] https://www.justice.gov/opa/press-release/file/982821/downlo... (pdf)