What you are portraying just simply isnt the truth.
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He did start at centre-back against Arsenal yes. The only game in the league he started as a centre-back. For the remainder if the season IF fit he either started alongside Gundo in midfield or benched him. In all games he were fit Fernandinho were preferred to start in his DM role
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He started against Newport, woth Gundogan being subbed on after 80 minutes
He only started on the bench in the semis against Brighton after a injury lay-off
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He started at CB in the first leg against Shalke granted, but was back in the pivot at White Hart Lane with Gundogan playing instead of a injured De Bruyne.
So he played twice at centre-back and started on the bench thrice after injury lay-offs in those 6 months. In every other game he was fit he was preferred over Gundogan, with Gundo either starting alongside him in midfield in De Bruynes absence or starting on the bench. Again, taking nothing away from Gundo but your version of events simply isn't true