I've just played it in my current save with Man Utd. All my players were knackered having just got back from international duty. Got 2 the QF and played Dortmund - I finished the game with 7 players (had 5 injuries, 4 were after I'd used all my subs) and Dortmund had just 6. Lost on pens. Game would've been called on IRL, so can only think this is a bug.