I not exactly sure what is going on - would you like to attach your dataset?
There are many possibilities that could explain this, namely
- Low resolution from level taxonomy summarization could obscure the signal, particularly if only one species is changing
- Low counts / zeros could cause false positives in ANCOM
- Issues with FDR in the statistical test
- A really bad fluke with the statistical test. Remember, we are just conducting statistical tests, and every statistical test has some chance of failing (even it is small).
Having access to the underlying datasets to generate this result could help narrow down these issues.