I have different sites on different hosting but always same issue. Some users when register do not receive confirmation email or is put in spam folder. Usually gmail work fine, live.com, yahoo etc not.
If it's only some users and it's random then it's very likely to be their mail server (probably going to spam folder) or it's your mail server (failure to deliver, etc..). Depending on how many emails you're sending you need to contact major mail servers like yahoo and have your domain whitelisted or you're going to go straight to spam after sending too many bulk emails (common with newsletters, etc..).
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