Were they interlinked? If so, then it is entirely possible. That's one of the main things Google says to not do & to stay away from.

I havent been deindexed and I dont interlink. But building alot of Affiliate sites right now and was wondering?

I personally think you should spread the risk. I am seeing evidence recently (google webmaster forums, my own members opening support tickets) of people being de-indexed en-masse for cookie cutter sites/MFA's etc. It appears Google may be having a purge, or has updated something to target them better.