The issue occurs when disassociating a product that is associated with multiple categories from a category. For example, after the Product is disassociated from one of two categories, the index still contains two ProductDocuments instead of one. This happens because the Incremental Index Update Strategy does not handle the Product Disassociation scenario. The full index rebuild removes obsolete ProductDocuments.
To resolve the issue for Sitecore XP 9.0 Update-2 with SXC 9.0 Update-3, download and install the hotfix available on this page:
SC Hotfix 339497-1 CommerceEngine 2.4.25.zip
Be aware that this hotfix was built specifically for SXC 9.0 Update-3. Do not install it with other SXC versions or in combination with other hotfixes, unless explicitly instructed by Sitecore Support.
Note that you must extract .zip file contents to locate installation instructions and related files inside it. Unless stated differently in the installation instructions, the hotfix must be installed on the CM instance and then synced with other instances using your regular development practices.
To get a solution for another SXC version, contact Sitecore Support.