Hi finley-finleygho,

The possible reason why some emails from QuickBooks Online were marked as spam is that the email domain of your customer blocks the @intuit.com. When they receive your email in their spam folder, you'll want to advise them to select This is not spam or Not Junk and then add [email address removed] to their contacts. This helps so that their email provider recognises the @intuit domain as a trusted site. 

You can also check on these articles for your reference:

Receive important email messages from Intuit

3 solutions for you when customers aren't receiving your emails

Feel free to message us back if you need further assistance. Thanks.