This is usually caused by the scanner being stopped manually. The result is that one echo won't have the same number of TRs written to the file. You can quickly check this with:
3dinfo -prefix -nt {$subj}_cmrr_mbep2d_bold_MEMB6_REST_*_e*.nii
That should return a list of all of the time point counts for each multi-echo run.
To also ask the other curious question: you have five echos, but are using the built in optimally combined function. Do you also plan to use tedana later?