Mine occasionally used to do this when at the pump. A solution I saw online worked. 
 

1. Lock the car with the remote

2. Apply GENTLE pressure to the fuel flap (pressing inward not pulling out) 

3. Unlock the car while still applying that gentle pressure to the flap

4. Release and open as normal

 

 

I eventually decided to replace the locking actuator. I have a 2014 SII estate.

 

My filler cap started to get stuck and did not open with the C/L last summer. Some pressure onto the flap helped though. I then opened the mechanism to regrease as the actuator usually worked with pressure onto the flap.

Last month I noticed that the flap was actually not locking anymore when the C/L was engaged. So I opened the mechanism again and strange enough it worked when I tested it and put some extra WD40 onto moving parts. The next day the flap was stuck in the closed position and would not open at all. I searched several forums for a solution and on a german Skoda forum one guy suggested to prise the flap open simply by pulling at the top of the flap with your fingers and working the C/L. The flap has enough play to get a finger in gently and the force seemed enough to the release it.

I then cut one of the wires and ordered a new actuator. I bought a cheap one on Ebay rather than going through the dealer. The part worked fine and I soldered it onto the cut wires rather than taking my boot liner off, although in another forum I read that one owner had cut the boot liner in the storage pocket to get a hand in and then unclipped the connector which sits at the bottom of the wheel arch.

I may have a new way of opening a stuck flap lock. I measured the resistance at the connector which was about 500 ohms: too high, but not open circuit. So I set my bench power supply to 30V and gave it a quick pulse and, hey presto, it opened. After multiple operations the resistance fell but to varying lower values. Some variation may be expected due to commutation but this looked excessive. I suspect the ubiquitous Mabuchi motor is on the way out. So a new unit is on order but I'm tempted to add wires so that a higher dc voltage can be applied without dismantling the interior. Hope this helps.

Edited 6 March6 Mar by Bartfarst

OK, a follow-up to my post earlier today. I went one step further and, in doing so, I reckon I've got to the real root of the issue.

Firstly, none of the white grease inside the unit had solidified to the point where it would impede movement of the mechanism. I removed and replaced all the grease I could find, but this was not the issue.

Having removed the Mabuchi motor I identified that throughout one rotational cycle of the motor, the electrical resistance across the terminals/connector varied significantly. Accordingly, I suspected either one coil of the armature might be open circuit, or that there was an issue with the commutator/brushes. So, I managed to peel back the two steel tabs holding the motor assembly together and then withdrew the front of the motor, which includes the commutator and armature, from the body containing the permanent magnets. I was then able to measure the resistances across the three armature coils, each of which was in the order of 6 - 7 ohms, balanced, and hence the armature was not at fault.

Peering into the narrow gap between the armature and the drive end of the motor I was able to see the brushes which looked complete and obviously had much life left on them. However, the commutator surface was heavily contaminated with carbon residue. Some of this I was able to remove with IPA on the stick of a cotton bud - the end of a standard cotton bud is too fat to get onto the commutator - but I was able to remove the remainder with a fine jeweller's screwdriver. I then reassembled the motor and ran it on the bench as 12V for a couple of minutes just to bed the brushes back in again. I then remeasured the resistance across the motor which came in a consistent 13 ohms irrespective of the rotational position of the armature.

I then reassembled the actuator body, supplementing the now broken clips holding the two halves together with a small zip tie. I then bench tested its operation again on 12V to confirm reliable operation. I then reinstalled the unit and put back the large amount of trim etc which had to be removed to access the connection to the main wiring harness. Hopefully this will now be good for another 160,000 miles!

So, the main conclusion is that, in my case anyway, degradation/contamination of the motor commutator was the root problem. On reflection, I personally doubt that spraying with WD40 etc would have penetrated sufficiently to have got to the inside of the motor, let alone cleaned all the contamination off the motor commutator. The process I've described is a bloomin' fiddly one, but I think it works. It also saved me three days wait and £51.30 which the local Skoda dealer wanted to charge for a new, OE item.

Hope this helps.

Thanks for the report Slarti 😄 - I'm a little surprised that a brushless servo isn't used for flap release.

Edited 6 March6 Mar by Warrior193
add emoticon

4 minutes ago, Warrior193 said:

Thanks for the report - I'm a little surprised that a brushless servo is not used for flap release.

In my experience the same little motors crop up widely across VAG products, principally in door locks etc.