During the past two years, a new ECR 2.45 GHz type ion source has been developed especially dedicated to intense light ion injector project like IPHI (Injecteur Proton Haute Intensité), IFMIF (International Fusion Materials Irradiation Facility), to reduce beam emittance at RFQ entrance by shortening the length of the LEBT. This new ALISES concept (Advanced Light Ion Source Extraction System) is based on the use of an additional LEBT short length solenoid very close to the extraction aperture. The fringe field of this new solenoid produces the needed magnetic field to create the ECR resonance in the plasma chamber. Such geometry allows first putting the solenoid at ground potential, while saving space in front of the extraction to move the first LEBT solenoid closer and focus earlier the intense extracted beam. During the commissioning of the source in 2011-2012, ALISES has produced about 20 mA extracted from a 6 mm diameter plasma extraction hole at 23 kV. But the magnetic configuration combined to the new extraction system geometry led to important Penning discharge conditions in the accelerator column. Lots of them have been eliminated by inserting glass pieces between electrodes to modify equipotential lines with unfavorable ExB vacuum zones where particles were produced and trapped. To study Penning discharge location, several 3D calculations have been performed with OPERA-3D/TOSCA code to simulate the possible production and trapping of electrons in the extraction system. The results obtained on different sources already built have shown very good agreement with sparks location observed experimentally on electrodes. The simulations results as well as experimental measurements are presented and solutions to prevent possible Penning discharge in future source geometries are established.