Hi @Katherine_Chau, It sounds like you're using cutadapt directly, not through QIIME 2. Please correct me if I'm wrong about that. Note that we are not the developers of cutadapt, so don't have a lot of expertise to help you out. Someone may jump in to help, but I would recommend reaching out to the cutadapt developers.
If you're working with ITS though, here are a couple of resources on the forum that you might find helpful:
Both are a little dated and may need some updates for more recent versions of QIIME 2, but hopefully this gives you somewhere to start if you want to work with QIIME 2.