What is the fuel temperature in the tanks during a flight? I'm trying to estimate the temperature of fuel stored in wing tanks during the flight. In my situation, I'm considering two wing tanks of 2000 liters each, one on each wing, at 20°C before the flight

I've run some calculations (I can provide additional numbers if necessary), and I end up with a temperature of 17°C after more than two hours of cruise (Mach 0.5, FL250)

Does this number sound correct to you? I was expecting a much lower temperature. I took a constant mass of fuel, which is not the reality, but even 15°C for instance seems rather hot. What are the usual temperatures of fuel in airliners tanks?
Quite cold, in fact.  External air temps at altitude reach -30 to -40 deg C.  The fuel in the tanks wil cool down and reach those temps within a couple of hours exposure.  Jet A has an icing inhibitor added to it to prevent freezing of the fuel in the tanks during extended periods in the stratosphere.

From a heat transfer standpoint, I would probably analyze this as a rectangular bar made from a composite sandwich of aluminum with a Jet-A center subject to convective cooling by air moving at a typical true airspeed, say 450KTAS at STP for FL250.  For simplicity we would ignore compressibility effects.  That may be where you erred.