Hi @bayegy,
Thank you for reporting this! I know just what the problem is.
This is not a common situation and you did not do anything wrong. This is a known bug that occurs when you combine certain databases with certain primer sets, resulting in some extremely short sequences. See this topic for a previous description and workaround.
The easiest thing to do would be to use the full-length 18S rRNA gene sequences, but another option is to remove the short sequences from the trimmed database (hint: D_0__Eukaryota;D_1__Opisthokonta;D_2__Holozoa;D_3__Metazoa (Animalia);D_8__Arachnida;D_9__Opiliones;D_10__Karamea lobata australis will be one of them! But there might be one or two others).
We have an issue to track this. This is on our radar to get fixed in the near future, so stay tuned for more details!