Strange as it sounds, what it is doing is correct.

Check with your state sales tax dept and you will find that CA has a hybrid sales tax scheme.  You collect sales tax based on the destination, but also collect your local city tax on the same sale

Resolution for 'County tax issue: 'Automated Sales Tax – charging the incorrect county – Why would shipping to Los Angeles from San Diego charge 1% San Diego County tax?' available: Yes.

The County tax issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the County tax issue yourself by looking for a resolution described in the article. If it is a complex County tax issue or you are unable to solve the issue, you may contact us by clicking here or by using other County tax support options.

For more information about resolving issues related to County tax in Quickbooks/QBO or to get support for the issue 'Automated Sales Tax – charging the incorrect county – Why would shipping to Los Angeles from San Diego charge 1% San Diego County tax?', click the link below: