I know this is an old thread but I'm just posting this for someone who comes 
along the same issue like me...

In order to fix my problem I had to do the following to fix for example the 
'ocspSigningCert cert-pki-ca' certificate renewing with wrong subjects:

Find the Serial number for that certificate:
#certutil -L -d /etc/pki/pki-tomcat/alias -n "ocspSigningCert cert-pki-ca" | 
grep Serial

Get the reqeustID:
#ldapsearch -D "cn=Directory Manager" -W -s sub -b 
cn={SERIALNUMBER},ou=certificateRepository,ou=ca,o=ipaca "metaInfo"

Get the request data:
#ldapsearch -D "cn=Directory Manager" -W -s sub -b 
cn={REQUESTID},ou=ca,ou=requests,o=ipaca

If the request data does not match the current certificate, we need to find one 
which should be used instead.
#certutil -L -d /etc/pki/pki-tomcat/alias -n "ocspSigningCert cert-pki-ca" | 
grep Subject
#ldapsearch -D "cn=Directory Manager" -W -s sub -b ou=ca,ou=requests,o=ipaca 
"extdata-req--005fsubject--005fname--002ecn={SUBJECT}"

If we have multiple results check the one which has the right attributes set 
comparing to a different system. Once you know which request to use change the 
requestid in the certificateRepository to the one selected. I used ldapadmin to 
connect to change but the ldapmodify should also work.

Hope this helps someone in the future...
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