Hi @elina2410,
Usually this happens when most, or all, of your sequences are oriented differently compared to your reference data. That is both your reference sequences and your data need to be oriented in the 5'-3' direction.
For more information see here.
One quick sanity-check, to see if this is the case, is to try feature-classifier classify-consensus-vsearch... as this approach does not care about orientation.
That being said, it might not be a good idea to construct a phylogeny as we're unsure if most, or all, of your reads are oriented similarly.