Set min insert size with -I option. Why do I still get proper pairs with insert size < min insert size?

[js72587]

I have used the -I parameter to set the mean, stdev, max, and minimum insert size instead of using BWA-MEM's insert size calculation. I've set it to -I 400,150,1500,100.

Setting the -I parameter, I would expect that pairs w/ insert size < 100 would not be flagged as a proper pair. However, I do get one mapped proper pair with the insert size 88. Am I misunderstanding this parameter? I did read from other forums that some people don't recommend using the "proper pair" flag, but I would still like to understand why this happens with the -I option and what I can do to set a minimum insert size correctly.

I would greatly appreciate any explanation on why this may happen with BWA-MEM. Thank you very much.