The car may have a problem with the diesel particulate filter or DPF, the purpose of which is to absorb particulate emissions (soot-like stuff) created when a diesel engine is started from cold. The soot is collected and stored in the DPF and then heated and burned off during one of the regeneration cycles, as dictated by the engine control unit, ECU, and emission control systems, ECS.
Generally, there are two types of DPF regen cycles, passive and active.
For the passive DPF cycle to work, the car needs to be a driven a fair distance regularly at motorway speeds (2k to 2.5k RPM) in order for the DPF to get hot enough to regenerate and safely burn off the particulates.
If the car does mainly short runs from cold starts and never warms up enough to trigger the passive DPF cycle, some cars have an active cycle where extra fuel is used to create hotter than normal exhaust gases to burn off particulates in the DPF.
Given the complex interactions required between electronic systems in diesel cars and these poorly thought out and often poorly executed pollution control systems, problems with DPFs are not unknown, even in well-engineered cars like Audi and BMW. It may very well be a Citroen software problem, but I doubt it somehow as a lot of the hardware and software is generic (from someone like Bosch or whoever).
All I can suggest is that you try taking the car for a long brisk run at the week-end and see if that helps. If it doesn't maybe someone can suggest a Citroen dealer or independent near you where the technicians know how to use and interpret the messages from the diagnostic equipment.
(I may of course be completely wrong, but it sounds disturbingly familiar.)