We experienced this behavior shortly after we set up our nurture programs, so in the Traffic Cop smart campaign, we set the Qualification Rule to "Each lead can run through flow once every 1 hour(s)", which helped cut down on multiple entries into the same nurture program's master campaign because a lot of leads have several trigger activities that qualify for the same nurture program during a short span of time. However if they triggered the Traffic Cop smart campaign later and qualify for a nurture program they are already in, they'd be in that program's master campaign twice at the same time as you are experiencing. Also it is possible that during the time that the lead is not qualified to run in the Traffic Cop smart campaign, he could have had an activity that would have caused the Traffic Cop to have directed him to a different nurture program's master campaign.
So not allowing the lead to run through the flow every time isn't the best solution and we did the following:
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Added a Nurture Program Assigned field to the lead records
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Added a Nurture Program Assigned "is not [this nurture program's name]" filter in the smart list of each nurture program's master campaign.
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Added a Change Data Value flow action with "Attribute - Nurture Program Assigned; New Value - [this nurture program's name]" in the flow of each nurture program's master campaign
So far the problem appears to be resolved.