When I’ve seen this error, it was due to not having intact pairs present in the input fastq files.
That isn’t a requirement always but ensuring intact pairs usually solves it. There is probably a specific option that is the trigger – but I don’t know for certain which 
So, if filtering by length isn’t enough (minimum seed length), try this to get rid of reads in either read dataset that no longer have a mate present in the other read dataset. In short, ensure that intact pairs are input to the tool. Some QA tools sort the outputs by paired/not state but others will just remove reads from one end.