The polymer Poly[(4,8-bis-(2-ethylhexyloxy)-benzo(1,2-b:4,5-b’)dithiophene)-2,6-diyl-alt-(4-(2-ethylhexanoyl)- thieno[3,4-b]thiophene-)-2-6-diyl)] (PBDTTT-c) p-doped with the molecular dopant tris[1-(trifluoroethanoyl)-2- (trifluoromethyl)ethane-1,2-dithiolene] (Mo(tfd-COCF3)3) exhibits a decline in transport properties at high doping concentrations, which limits the performance attainable through organic semiconductor doping. Scanning Electron Microscopy is used to correlate the evolution of hole conductivity and hopping transport activation energy with the formation of aggregates in the layer. Transmission Electron Microscopy with energy-dispersive X-ray analysis along with liquid-state Nuclear Magnetic Resonance experiments are carried out to determine the composition of the aggregates. This study offers an explanation to the limited efficiency of doping at high dopant concentrations and reinforces the need to increase doping efficiency in order to be able to reduce the dopant concentration and not negatively affect conductivity.