Hi Tanmay
We regularly apply DTIprep to multi band data. There should not be something particular about MB data regarding the QC process that's different from non-MB data. 

If the DWI volumes that get rejected by DTIPrep look visually free of intensity artifacts, then your DTIPrep parameters are likely to strict (DTIPrep's default parameter particularly for high b-value images can be too strict). Adjust the parameters of the steps that fails your DWI volume.

Not sure about the distortions, to me it looks like that the voxelsize information in the volume may be incorrect as it seems stretched in inferior-superior direction (or at least incorrect the way AFNI displays it, does it look similarly in fsl if you use fslview, or in Slicer?). It is possible that your acquisition uses a slice overlap and thus that the voxelsize in the slice-direction has been set to the DICOM slice thickness instead of the slice step (difference in slice-position between slices).

Martin