Slavia Prague won the second-leg of their round of 32 tie 2-0 to reach the round of 16 on aggregate 2-0.
Schmeichel said: "It's very disappointing, but I do not think we can complain so much. I think we have to be honest with ourselves and say that seen over the two matches, it was probably the best team that won. It's just a shame.
"They did a really good job. We started well, but then they increased their intensity in the pressure, which gave us trouble holding on to the ball. In the second half they went for it and we were not quite as aggressive as we should be, which is very disappointing."