You have Opportunities in Salesforce but they are not showing in Marketo. You are unclear why this is happening.
1) Check Opportunity permissions in Salesforce - Your first line of troubleshooting this issue is to ensure that the Salesforce profile being used by your Marketo sync user has the Create/ReadEdit/Delete access on the Opportunities object in Salesforce.
2) Check the "Contact Roles" Related List - Ensure that the "Contact Roles" Related List in Salesforce under the Opportunity's detail page is populated
3) Ensure that the Marketo sync user has visibility in Salesforce to see the Opportunity - Log in to Salesforce with the Marketo sync user and ensure that the missing Opportunity in Marketo is visible to this Marketo sync user. If the Marketo sync user can't see the Opportunity then the Opportunity will not sync to Marketo.
4) Check to see the time that the Opportunity was created in Salesforce - Often times you have all the correct Opportunities permissions in Salesforce but the Opportunities are still not showing in Marketo because the Opportunity was recently created and you have not allowed enough time for that Opportunity to sync to Marketo. In this scenario, the only thing you can to is wait. If your sync is busy processing other items, you usually need to wait for these pending items to sync before the newly created Opportunity will sync to Marketo.