CNAMEs are name-level aliases. So if for example I make the following query;

  name=www.example.com type=A

and get a response of the form;

  www.example.com 3600 IN CNAME www.example.org 

a resolver will then recurse and lookup name=www.example.org, type=A. The CNAME indirection is cacheable for all queries to www.example.com though, of any type. So if I make a query for;

   name=www.example.com type=AAAA

the resolver can skip any query to the nameservers for www.example.com and go straight to a query for name=www.example.org, type=AAAA. So in effect a CNAME "masks" all records of any type, for a given name.

At zone-apexes this becomes a problem. Zone apexes are required to have SOA and NS record sets which play important roles in record-not-present responses and nameserver discovery respectively. Another problem is masking MX records, but you could always copy the MX records at the target name to work around that.