Trimmomatic trims most of the reverse strand
Maybe you need to remove the unpaired reads:
trimmomatic PE -phred33 -threads 2 \
    read1.fastq.gz read2.fastq.gz \
    read1_trimmed.fastq.gz read1_unique.fastq.gz \
    read2_trimmed.fastq.gz read2_unique.fastq.gz \
    LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15

Then you can try with bwa.