What version of Hugo are you using (hugo version)?

$ hugo version
hugo v0.120.4-f11bca5fec2ebb3a02727fb2a5cfb08da96fd9df+extended darwin/arm64 BuildDate=2023-11-08T11:18:07Z VendorInfo=brew

Does this issue reproduce with the latest release?

1. Create a categories taxonomy.
2. Create file /categories/a/_index.md and /categories/b/_index.md
3. Create posts for those categories.
4. Add the following to your config:

[permalinks]
  categories = '/:filename/'

All categories will be concurrently built to /index.html, which leads me to believe that :filename is empty for them.