Is that your own self-signed root CA, or an older Verisign V1 Root CA or similar? Because that would generate a warning. From the manual (emphasis mine)
The basicConstraints extension CA flag is used to determine whether
the certificate can be used as a CA. If the CA flag is true then it is
a CA, if the CA flag is false then it is not a CA. All CAs should
have the CA flag set to true.
If the basicConstraints extension is absent then the certificate is
considered to be a "possible CA" other extensions are checked
according to the intended use of the certificate. A warning is given
in this case because the certificate should really not be regarded
as a CA: however it is allowed to be a CA to work around some broken
software.
If the certificate is a V1 certificate (and thus has no extensions)
and it is self signed it is also assumed to be a CA but a warning is
again given: this is to work around the problem of Verisign roots
which are V1 self signed certificates.
The code=3
might have to do with the fact that X509 v3 extensions are missing. At least that is what a quick scan of the code suggest:
./crypto/x509v3/v3_purp.c
:
/*-
* CA checks common to all purposes
* return codes:
* 0 not a CA
* 1 is a CA
* 2 basicConstraints absent so "maybe" a CA
* 3 basicConstraints absent but self signed V1.
* 4 basicConstraints absent but keyUsage present and keyCertSign asserted.
*/
Downloading a couple of the old VeriSign root certificates complete reproduces your warnings:
wget https://www.symantec.com/content/en/us/enterprise/verisign/roots/Class-3-Public-Primary-Certification-Authority-G2.pem
openssl x509 -purpose -in Class-3-Public-Primary-Certification-Authority-G2.pem
Certificate purposes:
SSL client : Yes
SSL client CA : Yes (WARNING code=3)
SSL server : Yes
SSL server CA : Yes (WARNING code=3)
Netscape SSL server : Yes
Netscape SSL server CA : Yes (WARNING code=3)
S/MIME signing : Yes
S/MIME signing CA : Yes (WARNING code=3)
S/MIME encryption : Yes
S/MIME encryption CA : Yes (WARNING code=3)
CRL signing : Yes
CRL signing CA : Yes (WARNING code=3)
Any Purpose : Yes
Any Purpose CA : Yes
OCSP helper : Yes
OCSP helper CA : Yes (WARNING code=3)
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----