In combining spin- and symmetry-resolved photoemission, magnetotransport measurements and ab initio calculations we detangled the electronic states involved in the electronic transport in Fe(1-x)Co(x)(001)/MgO/Fe(1-x)Co(x)(001) magnetic tunnel junctions. Contrary to previous theoretical predictions, we observe a large reduction in TMR (from 530 to 200% at 20 K) for Co content above 25 atomic% as well as anomalies in the conductance curves. We demonstrate that these unexpected behaviors originate from a minority spin state with Δ(1) symmetry that exists below the Fermi level for high Co concentration. Using angle-resolved photoemission, this state is shown to be a two-dimensional state that occurs at both Fe(1-x)Co(x)(001) free surface, and more importantly at the interface with MgO. The combination of this interface state with the peculiar density of empty states due to chemical disorder allows us to describe in details the complex conduction behavior in this system.