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Reports, including Email Program dashboards, have "implied" actions.
To track opens, Marketo adds an invisible tracking pixel to every email. When images are downloaded in an email, this tracking pixel is downloaded from the Marketo server and Marketo marks an open. However, it is possible to click on an email without downloading the images. In this case, Marketo will add an "implied open" as it is not possible to click on an email without opening it. This will add an opened to the report. However, since the images were not actually downloaded, an open activity will not appear in the leads activity log. Thus, these leads add an opened to the report but will not appear in a Smart List of opens.
Reports also are not affected by leads being deleted or merged. So some of the descrepency could come from leads who clicked/opened on the email either being deleted or merged together.