If you don't use a deliverability tool like Litmus I strongly recommend that you look into it. Email Testing and Rendering Previews - Litmus Yes it will cost a small amount of money but it is absolutely worth it! Your emails going into the Junk Folder can happen for a wide variety of reasons. I'd recommend looking more closely at your email deliverability rates in Marketo. You should also do an analysis of people in your Marketo database with a email @hotmail.com -- run a report and do a spot check on deliverability error codes. If you are seeing a lot of error code of 550-559 you maybe repeatedly sending to what appears to be a "bad email address" from a system perspective. Marketo does offer some protection for this -- however, I don't know how many times Marketo will attempt to send to an address with 550 deliverability error code before it sees it as an undeliverable address. I'd recommend logging a support ticket and have a conversation with Marketo support - and give them a copy of the report on hotmail accounts going to spam. If you have hit a SPAM trap Marketo may be able to do to help you resolve any issue that could impact sender reputations.
Here is some info you may find helpful: What Those SMTP Error Codes Mean and Why You Should Care | Getting Email Delivered
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