Question: What could be the main reasons for a short-haul flight to be delayed over an hour in-flight?

Recent [Lufthansa LH 2227 CDG-MUC flight](https://www.flightstats.com/v2/flight-tracker/LH/2227) took off only half an hour after scheduled time, but landed at destination delayed nearly an hour and a half.

[![enter image description here](https://i.stack.imgur.com/CgeTZ.png)](https://i.stack.imgur.com/CgeTZ.png)

Meaning (if I am reading these stats correctly) that this particular flight spend an hour extra in the air over scheduled time. I begin to question if there is enough fuel for the plane to stay that long extra?

I flew the very same flight few days ago and that flight also took of half an hours after schedule and landed fifteen minutes after schedule. Meaning that a plane manage to "work out" half of its delay en route. This particular, pictured flight not only didn't work out its initial delay, but also added another hour to it while being in air.

I was always told (and saw that in my small commercial flying experience) that 

* short- or middle-haul flights delayed 15-30 minutes on take-off,
* long-haul flight delayed 60-90 minutes on take-off,

are nearly always able to land on-time, effectively "working out" their initial delay during flight, by flying faster etc. What happened or could happen here?

Answer: 
If you look at the details, you’ll see the aircraft left the gate at 9:37, but only took off at 10:47.

They probably received notice of [the issue in MUC pointed out by Machavity](https://aviation.stackexchange.com/a/68146/3313) while taxiing to the runway (and then asked to park somewhere waiting for the airport to be ready for them). No sense returning to the gate for a delay like this which is expected to be relatively short.

A possible alternative (though probably not here) is they they had an issue right after gate departure which triggered a maintenance request. It happened to me once on some regional airliner which had an issue just when they spooled up the engines (or just after a few meters, don’t remember). Immediately powered down and had some part of the engine changed (or maybe just a filter or something similar) while we were waiting, took about an hour or so.
re 'working out delays' 

The flight uses an operational flight plan which shows the routes (waypoints), speed, altitudes. There are usually some compromises made, a shorter route may cost more (overflight fees) and a cheaper route may take longer. The company will usually select what is best ie more economical with flight time acceptable.

In exceptional cases like longer delays, the ops dept may choose a higher cost route to minimise the impact (more direct route or higher cruise speed). This is usually easier to do on longer flights of course, on shorter routes there may not be much choice.