I was having problems with some files remaining after I clicked Run Cleaner. I would click Analyze again, then click Run Cleaner and the same file or files were still on the list.
I finally figured out through Trial & Error, that if I clicked Run Cleaner again it deleted more files. I clicked Run Cleaner again and more files appeared on the list showing which files I deleted that time.
Now I click Analyze once and Run Cleaner until it shows "0 bytes removed".
You have a rule for Prefetch? I use the standard checkbox (remove entries older than 14 days) and it works fine. If you have a rule for Prefetch perhaps it's conflicting with files in use or some other restriction.
Perhaps CC applies the same rules to the included prefetch folder as it does to the prefetch entry in Cleaner/Advanced. After all prefectch is supposed to be a boot and program load speedup tool.
When I added the prefetch folder to my Include entries all prefetch files were listed on an Analyse. I'm not going to run it but I would bet that it removes the same amount of files that the Cleaner/Advanced option does.
If you're so worried about prefetch just change the registry option so that no application, or even no boot time application, are created. How to do it is Googlable.
This prefetch thing will be argued about til the end of time . As far as I am aware Windows has a limit of 128 entries (1024 entries on Win 8 and 8.1) and then after adding a new entry, drops the last one. I guess it was important for XP but newer operating systems use them more but in a different way.
If you want to look at it forensically jump in here