The APS did not intercept the 9M123 even though it should have
In the list of hits to the top left in the first screenshot you show they you’ve been hit twice within 3 seconds. In your second screenshot you can see that the APS list only one countermeasure loaded (at the bottom of the info for the APS). So i’m guessing that it had already used the countermeasure against the first missile and had no countermeasures left for the second one.
oh, i did forget to show the first hit, it did end up penetrating knocking out the driver engine and transmission
Do you have a link to the server replay?
That does look a bit odd yeah, kind of hard to tell angles though. But i would report that one on the CBR. You can bug report it here (just search a bit first so that you don’t report something that is already reported and known about): (Gaijin.net // Issues)
A guide on how to report bugs can be found here: ([Navigation] Technical Knowledge Base | War Thunder Wiki)