Well that is what would happen if transparent... if one is failing is because it tried to resolve normally and it failed.
PM me the details of domains and example what you queried that did not fail on one, etc
local domain sub.domain.tld, transparent. And you query something.sub.domain.tld and no record of that locally then it will try and resolve that normally.. Which may or maynot get you a response.
If you do not want anything to be resolved normally in this domain your using locally then you would set the zone type to static.
Using a domain locally that is public as well can lead to unwanted sort of responses.. Especially if you do not control the public NS for this domain.