It could be all manner of reasons as to why the bags were not loaded, they range from:
1. A possible industrial dispute at MUC
2. Baggage belt failure at MUC
3. Flight crew possibly close to going out of hours
Did you actually ask the Swissport representatives as to why the bags hadn't been loaded? If you did, and they didn't know, why didn't you ask them to 'jolly well find out?'
With regards to the fact that the bags were loaded onto a flight later on in the evening, well that isn't a problem as the aircraft (assuming it was an Airbus 319?) has 2 baggage holds, normally only the rear hold would be used, but in exceptional circumstances the forward hold will be used - as long as the pilots are aware that baggage is in both holds then it isn't a problem.