Sounds like you are having similar issues to this forum post. The 99% classifier is obviously working, as many of your features are being classified deeply.
There is also a very clear pattern here that suggests that you have the same problem as described in that other thread (non-target DNA): the closed-reference OTUs (these have numbers as IDs) are all classified, but none of the open-reference OTUs (IDs are long strings of letters/numbers) are being classified.
I recommend BLASTing some of the unclassified OTUs to see if they match to, e.g., host DNA (e.g., if your samples are from human, mouse, plant). PhiX may be another issue. Check out that other forum post for a good discussion of:
- different problems that can cause this issue
- how to diagnose the problem
- how to fix the problem by filtering
- how to prevent the problem to begin with (e.g., with deblur or dada2)
I hope that helps!