Reply to Marketo Emails are going to spam folder

I've seen this happen too! Not sure why or how, thought it was just our instance.

There are a lot of things that affect deliverability, I'd be interested to know if your emails are also going into spam folders or if its only their replies. This likely has to do with the IP addresses Marketo is using to send emails for your instance of Marketo. Have a call with their email deliverability people - if your emails go into your spam folder, they're probably going into your lead's spam folders too.

The initial email is not going into the spam folder, only the replies from leads. 

This has happened to us a few times. In many cases, it's because the IP Address Marketo is using for our company has been added to a spam blacklist. It is a good idea to give your Marketo deliverability person a call.