Error with BWA Mem input having multiple fastq files using cat and process substitution
You are correct that the concatenation of input read files will confuse BWA. BWA depends on the input reads being in the same order in R1 and R2 files for paired-end alignment. 

From bwa docs: If mates.fq is present, this command assumes the i-th read in reads.fq and the i-th read in mates.fq constitute a read pair. BWA will not search through FASTQ files trying to find matching mate IDs. 

You will notice that your initial error message is reporting two different read IDs that are improperly paired. Presumably the mispaired read corresponds to the first read in the out-of-order file.