Off topic:Samtools SORT or bedtools bamToFastq giving error when converting reads to fastq.

Question

[DNAngel]

I am trying to convert mapped reads and unmapped reads into fastq format but I am having trouble with the last bit of my pipeline.

Here is my pipeline:

bwa index refgenome.fa
bwa mem -B 2 -M refgenome.fa cert1.R1.fastq cert1.R2.fastq > cert1_aln.sam
samtools view -Sb cert1_aln.sam > cert1_aln.bam

# I do a sort here but maybe I don't need to? I have just seen many pipelines that sort and index at this point so I did it too.
samtools sort cert1_aln.bam > cert1_aln_sorted.bam | rm -f cert1_aln.bam
samtools index cert1_aln_sorted.bam

# Gather some stats
samtools flagstat cert1_aln_sorted.bam > cert1_stats.txt

# Extract unmapped read whose mate is mapped
samtools view -b -f 4 -F 264 cert1_aln_sorted.bam > cert1_tmp1_unmapped.bam
# Extract mapped read whose mate is unmapped
samtools view -b -f 8 -F 260 cert1_aln_sorted.bam > cert1_tmp2_unmapped.bam
# Extract unmapped read with unmapped mate
samtools view -b -f 12 -F 256 cert1_aln_sorted.bam > cert1_tmp3_unmapped.bam

# Merge the three tmp files into 1
samtools merge cert1_unmapped.bam cert1_tmp*_unmapped.bam

# Extract mapped reads from BAM file
samtools view -b -F 12 cert1_aln_sorted.bam > cert1_mapped.bam

# Sort the BAM files by name
samtools sort -n cert1_unmapped.bam > cert1_unmapped_sorted.bam
samtools sort -n cert1_mapped.bam > cert1_mapped_sorted.bam

# Finally, convert to Fastq
bamToFastq -i cert1_unmapped_sorted.bam -fq cert1_unmapped.R1.fastq -fq2 cert1_unmapped.R2.fastq
bamToFastq -i cert1_mapped_sorted.bam -fq cert1_mapped.R1.fastq -fq2 cert1_mapped.R2.fastq

I am getting an error somewhere in between sorting and converting this is the error I am getting and it crashes my terminal every time:

 someseqname is marked as paired, but its mate does not occur next to it in your BAM file. Skipping

The above error is ENDLESSSS just spams my entire terminal and does not stop. My fastq files that I do end up with are incredibly tiny. I tried sorting without the -n flag and with it, same issue each time. I also tried using the header flag with samtools view when extracting the reads (ex: samtools view -bh -F12) but no luck...why is this happening?