The Trophy Active Protection System (APS) is currently not performing as expected. It inconsistently fails to intercept incoming threats such as ATGMs, and even when it does activate, the protected vehicle often still suffers significant internal damage. This includes destroyed breeches, injured or dead crew members — even from relatively moderate and slow threats like the TOW-2 missile.
You can test this yourself (if you have a vehicle with the Trophy APS) in the test drive.
Might be something also to do with the HEAT chemical jet changes they did, whereby HEAT rounds detonating prematurely still form a damaging jet (like they had penned a vehicle). It may be that this jet is forming despite being intercepted by APS.