QB Issue Resolution:

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 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 (Solved).
Source: Intuit Community forum.

Automated Sales Tax – charging the incorrect county – Why would shipping to Los Angeles from San Diego charge 1% San Diego County tax?: this 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 issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Automated Sales Tax
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Error Recovery for Automated Sales Tax [Canada]
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