Yes he struggled, but most Centre Backs don't enjoy being auxiliary Full Backs. Also he hadn't had much game time so in effect we played an off the pace player, out of position, in an away cup tie; so it should be of little surprise he struggled.
The failing here is not Boyata's, but the Management Team's.
From a layman's perspective, there seems little point in having an EDS system, if at the point where you don't want to play your one fit Right Back (Zabaleta) it cannot supply a suitable replacement to step forward to the 1st team?
If this 'stepping-up' is not considered possible then can somebody explain why we are bothering building that Academy?
Ask yourself this, if Hart, Pantilimon and Wright got injured, would you accepted the management putting Ferandinho in net rather than go to EDS level to use Gunn?
Well the simple answer is No, so why did the management think playing an 'off the pace' Centre Back out of position as acceptable tactic?
In short, Boyata didn't play well, but he did as well as he could. The reason the team struggled was that he was asked to something he couldn't, and that is a fault of the management.