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This is a clone of the https://bugzilla.redhat.com/show_bug.cgi?id=1112767
Please read the details there. 

While we think that documentation needs to be more clear we also should make some usability changes. For example instead of just failing and saying that there are more than one cert in the file we should say something like:

There are more than one certificate detected.
Subject names:
foo
bar
baz  
rerun the installation adding an additional argument --some-arg-to-choose-the-cert = <subject name from the list above>

Upstream ticket:
https://fedorahosted.org/freeipa/ticket/4489

We decided to track this fix in other tracker - Bug ​1129558.

*** This bug has been marked as a duplicate of bug 1129558 ***