Is this acceptable to you? Or let me put it in a more appropriate way, it this acceptable to you if you were the victim and your team got knock-out of C-L or Cup or failed to win the final because of such anomalies?
There is definitely something 'fishy' going on. It could be intentional or it could be a malfunction or flaw. It could be due to the 'roll of dice' like Nik said, or it could be due to something else in this game or a combination of several things. For sure though, there is no football logic in the outcome of many cases that are similar to the above.