Homocoupling defects in conjugated polymers often go undetected but may cause significant batch-to-batch variations that ultimately give seemingly identical polymers different material properties. These defects may go easily unnoticed because conjugated polymers are commonly characterized via gel-permeation chromatography and elemental analysis, two techniques that are not able to provide information on monomer incorporation or end groups. Nuclear magnetic resonance spectroscopy has provided evidence of homocoupling defects, but is limited to polymeric repeat units with distinct chemical shifts and little spectral overlap, a luxury unavailable in polymeric dioxythiophenes. Here, matrix-assisted laser desorption/ionization timeof-flight (MALDI-TOF) mass spectrometry (MS) was used to characterize different dioxythiophene copolymer (PE2) batches based on 3,4-propylenedioxythiophene (ProDOT) and 2,2'-bis-(3,4-ethylenedioxy)thiophene (biEDOT) to elucidate changes in structure within different polymer batches. It was determined through the analysis of MALDI-TOF mass spectra that excess biEDOT is incorporated into PE2 when using standard direct (hetero)arylation polymerization (DHAP) conditions. It is hypothesized that the high nucleophilicity of biEDOT causes uncontrolled concerted metalation-deprotonation steps in the DHAP catalytic cycle at high temperatures. To improve control of the biEDOT incorporation, the reaction temperature was lowered from 140 to 80 degrees C, and a different polymerization procedure was used where the reaction temperature was ramped-up from room temperature. Ultimately, incorporation of excess biEDOT was advantageous to the conductivity of oxidatively doped polymer films, with values greater than 200 and 80 S/cm for the high- and low-temperature polymerizations, respectively. This work correlates small differences in polymer structure with solid-state conductivity to expose how batch-to-batch variations regarding homocouplings can produce different material properties.