This happened when users ran snyk monitor with the --project-name option before it was supported for snyk test.
The --project-name option overrides the default project name, so if the default project name is goof but you specify a project-name of goofy, snyk looks for a project called goofy and applies the .snyk policy for that project. Before the option was supported for snyk test snyk did not find a .snyk policy for the default project goof and therefore did not apply the ignores.