Since 2016 Account Engagement (Pardot) allows multiple prospects with the same email address (AMPSEA) and therefore the email address is not any longer the unique identifier. If you have an account created after June 2016 this feature is activated by default and can't be reversed. This change has implications for how Account Engagement handles incoming data. The following review summarizes the most important implications. You can find the official Salesforce document here. 

4 Matching Rules for Prospects with existing Records 

Prospect Import
In terms of imports, Account Engagement offers the possibility to choose between CRM ID and email address as matching criteria. It is recommended to use CRM ID. But if you choose email as the matching criteria and the email address of an incoming prospect matches with more than one existing prospect, Account Engagement adds the record to the one with the most recent activity.

Form Submissions
After a form has been submitted, Account Engagement tries to associate the activity with a prospect via a visitor cookie. If the form has been submitted by a visitor with a corresponding visitor cookie, the activity is added to this record. If the visitor cookie matches with a prospect in the recycle bin, it is undeleted. For prospects with no corresponding visitor cookie, Account Engagement looks for corresponding email addresses. If there is more than one prospect with the same email address, the incoming activity is saved to the prospect with the most recent activity. If there is no prospect with a corresponding email address, Account Engagement creates a new one.

Third-Party Connectors
In terms of syncing data from a third-party connector, Account Engagement looks for corresponding email addresses. If more than one prospects have the same email address, Account Engagement adds the incoming record to the Prospect with the latest activity. If there is no corresponding email address, Account Engagement creates a new one and adds the incoming activity.

Salesforce Connector
The Salesforce connector is based on a 1 to 1 relationship between a Account Engagement prospect and a Salesforce lead, contact, or person account. In this case, CRM ID is used as the matching criteria for syncing in both directions. 

3 Handling Rules for multiple Prospects with the same Email Address

Email Sending Rule
If multiple prospects on an email send list have the same email address, only the prospect with the latest activity receives the email.

If there is more than one prospect on the email list and if one of them is on a suppression list, the email is not suppressed, because Account Engagement suppresses based on prospect ID. There is an exception to this rule. Account Engagement uses email addresses for dynamic suppressions based on recency and frequency. In this case, all prospects with the same addresses are suppressed.

Opt-Out Rule
If a prospect globally opts out, all prospects with the same email address are marked as opt-out. If a prospect unsubscribes from specific email lists, all prospects with the same email address are unsubscribed from those lists. If a prospect hard bounces or soft bounces five times, all prospects with the same email address are marked as unmailable.

Engagement Programm Rule
In terms of Account Engagement's engagement programs, there is only one prospect per email address per program. This means that email addresses with multiple prospects only get one copy of the same email. 

AMPSEA has triggered quite a controversy about the usefulness of this feature. But whether you like it or not understanding the rules of AMPSEA is important. If you have any further questions feel free to contact us.

Reference

https://help.salesforce.com/articleView?id=pardot_admin_ampsea_parent.htm&type=0