I have had this problem a couple of times now (incorrectly ordered permissions)
I started with a pool made from three freshly formatted drives. I turned 2x duplication on and copied a whole load of files to the pool.
I thought I would have a little play so changed duplication to 3x. At the end of the duplication pass drivepool flagged it had had problems with some files - not able to get oplocks on them so implying they were in use. On looking at the specific files they were family photos in a folder that had not been accessed by anything that I could think of**(see edit) so I just clicked the duplicate now button and thought nothing of it.
After this pass it again said it couldn't get oplocks on the files. On looking a bit closer, Windows complained that the permissions on the folder that contained the files were incorrectly ordered. Now, this is a bit odd as there are several hundred files in the folder and as far as I can see Drivepool is only complaining about a few of them (although it may be not showing the full list of course).
Now, I am fairly sure that the permissions were okay when the files were copied to the pool - indeed that were copied from an external HDD with a FAT partition so no NTFS permissions should have been copied.
This is actually the second time this sort of thing happened to me. The first time I just fixed the problem and put it down to cosmic rays or something but now it has happened again I am wondering if there is something in DP that might be a teeny bit awry.
WIndows 8.1,
DP Version StableBit.DrivePool_2.1.1.561_x64
Edit: Not strictly true. The folder in question was shared and files (pictures) were being displayed by an HTPC screen saver, but I don't think this invalidates the permissions - the files were not being modified and the folder permissions were not accessible to any other device as the folder was the item shared and therefore not seen by "share-ees". The permissions were wrong on the folder and inherited to the files.