The Marketo connector for Microsoft Dynamics doesn't check for matched Marketo records when a new record is sync'd from Dynamics. This can create havoc in your database if you have many Marketo only records.
Here are a couple of scenarios outlining how duplicates may be being created:
Scenario 1: Marketo only record and new lead from DCRM
Scenario 2: Duplicates from DCRM
Scenario 3: Matching Lead and Contact from DCRM create duplicates in Marketo
To help prevent these scenarios I suggest you sync all of your DCRM records with Marketo so that any form completions or imports into Marketo will match the existing record and not create duplicates, and you sync all of your Marketo records with DCRM and enable Duplicate Detection Rules in DCRM.
Here is how to set up duplicate detection rules:
Step1: Navigate to Data Management
Step 2: Select Duplicate Detection Rules
Step 3: Select New
Step 4: Define the rule, save and close
Step 5: Publish the rule
Here are the rules I would suggest you begin with:
If you need to support duplicates in DCRM and you've setup the sync filter field in DCRM and you can prevent them from being sync'd with Marketo by setting their SyncToMkto field to "no".
Share your experiences in managing duplicates in the comments here - I am sure there are many alternate approaches out there!