I assume you mean that it is not working when they are not oriented the same way as the reference database. 
Keep this in mind when trying to generate ASVs / OTUs and constructing a phylogenies. You might get spurious results the reads are of mixed orientation. So, you'd need a way to orient all of the reads in the same direction.
Sadly there is no way to, currently, orient fastq files in QIIME 2. Though it should be possible via running vsearch manually outside of QIIME 2, then re-importing. See here for one possible approach.
You can use qiime rescript orient-seqs ... to orient FASTA sequences.