There are many implied steps in Mareto that will synch the lead to SFDC including change lead owner, add to campaign etc. And in any of these flow steps, Marketo will either update the existing record or insert the lead and then update the information.
You might want to look at your Marketo de-dupe criteria; are you using default email address for de-duping in Marketo or do you have custom criteria? It's important to look at that so you know which system- SFDC or Marketo is doing the de-dupe.
Hope this is helpful.
Avnita