Alex,
Typically this occurs when you have identical hostnames set for some of your domains. Consider this:
1. I set my domain default hostname to mail.test.local, which is also the hostname of the test.local domain
2. I create 2 new domains, new.local and newer.local, which will have mail.test.local as their default hostnames
3. If I check automatic certificates, I'll have 3 mail.test.local certificates, although if I double click them, i can see they are bound to different domains(test.local, new.local, and newer.local, respectively).
This is expected behavior when using duplicate hostnames, but it shouldn't cause any issues! If you want to prevent this behavior, I'd set the default hostname for domains to mail.%domain%, which will prevent duplicate certificates, instead generating a unique set per domain.
I hope this helps!
Jorel Haggard
System/Network Administrator
SmarterTools Inc.
www.smartertools.com