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I gather from what you write that your smart campaign is sending emails and that have lead/contact duplicates (with the same email address) and therefore they receive the email since the SFDC Type = contact filter does not exclude the leads.
There is not much you can do about it as Marketo does not allow easily to cross reference records. You could create a smart list of duplicates that are also contacts, export the list of email addresses and add them to an excluding list (email address is not ...) but this will require and export each time you want to shoot your campaign. Not very convenient...
The truth is that having lead/contact duplicates is something you need to address through revision of your lead management process + the addition of duplicate control in SFDC to prevent this from happening. In the same time, you should consider merging them in SFDC (through a conversion of the leads). You can also consider investing into a duplicate cleansing tool that can work in SFDC and merge these duplicates automatically.
The last thing that can be done is an SFDC trigger on leads that checks the database for existing contacts with the same email and flags the leads in that case in a dedicated field that you sync to Marketo. Then you filter out these leads on this fields.