Sprout Forms or Craft not sending email to Craft user email addresses
As mentioned in the comments, this is likely an email configuration issue and Brad's comment should be taken to heart:


  both sendmail and PHP's mail are notoriously unreliable and shouldn't be used in production environments


Craft should not be treating user emails differently than non-user emails and Sprout Forms isn't doing anything unique when it sends notification emails, it's just piggybacking on what Craft is doing.

Sending your email through a service like Mailgun (or any similar service) will give you more visibility into what's happening and what you may need to troubleshoot. Sprout Email has a Sent Email Element Type that you can enable to help troubleshoot some email deliverability issues on the Craft side of things.

For two good overviews on troubleshooting email errors in Craft, see:


https://craftcms.com/support/troubleshooting-email-errors - Craft Docs
Troubleshooting and debugging errors in PHP - Straight Up Craft




Another direction to consider when troubleshooting an error like this may be to look closer at the From headers and what emails you are sending to. Is it really just Craft Emails vs non-Craft Emails or could there be other patterns? For example, maybe the emails that aren't being received are all gmail addresses. In some cases, if you are sending to a gmail address you own from a gmail address you own, Google may suppress the email from appearing in your inbox.