vS - I don't have any exact references but if you'll check out the KTB's and "uboatarchive" (http://www.uboatarchive.net), you will see many records like "the Boat left port on this date but had to return due to noise caused by ..."

Many times, the problem is noted as being a bent propeller or drive shaft (also, bearings, engine clutches, etc. but props and shafts are the big things). Propellers on most typs of U-boats weren't very well protected (cages and deflectors were small and light-weight) and would have been easily damaged by floating debris, cables, bumping into docks or armored pens, striking the sea floor, etc. Since they were so easily damaged, I'm guessing that many sailed with small dents and "dings", but certainly the larger damages would need to be repaired.