Hello Rachel,
Welcome to the forums! 
Thank you for including ALL the details in your post. This is very helpful!
I think these two things are related: binned quality scores 
and
Error rates could not be estimated
Take a look at this thread from the DADA2 developer: NovaSeq and Dada2 incompatibility. - #12 by benjjneb
Also check out the alternative methods outlined here: NovaSeq data in QIIME2
Keep us posted on your progress and what you try next!