BBDuk quality filtering not producing expected results

I’m trying to trim/filter low quality reads from paired-end exome-seq data, using BBDuk.

I used the command:

for ea in $files; 
    do 
    R1="$ea"
    R2=$(echo $R1 | sed "s/R1/R2/")
    /home/shared/programs/bbmap/bbduk.sh -Xmx1g in1=$R1 in2=$R2 
    out1="$(echo $ea | sed s/.fastq.gz/_trimmed_filtered.fastq.gz/)" 
    out2="$(echo $(echo $ea | sed s/R1/R2/) | sed s/.fastq.gz/_trimmed_filtered.fastq.gz/)" 
    ref=/home/shared/programs/bbmap/resources/adapters.fa 
    t=10 ktrim=r k=23 kmin=11 hdist=1 maq=10 minlen=60 tpe tbo
  done;

After running fastqc on the output of this, I’m seeing that R2 files have some reads with low quality scores (see per sequence quality score), and the overrepresented sequence “NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN”, which should have been filtered out by quality filtering, no?

Any help here would be much appreciated.