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Where was the email sent from?
If it was a nurture campaign, then removing someone from the list your used to add them to the program would not have removed them from the program itself. They would still be members of the stream until you run a flow action to pause them or change their program status to Not In Program.
If the email was sent through a smart campaign with wait steps, then the same thing applies. Once a lead is qualified for your smart list, removing them from the list, or any lists that were referenced, would not remove them from the flow of the campaign.
If it's not a dupe (see Priyank answers) then John's cause is right. You can remove someone from a smart campaign with wait steps with a "remove from flow" flow step.
Hope this helps,
I think you had dupes for the same lead which you merged later, I think you need to check Lead' activity log. This might be one possibility.