"mostly". It's not unusual to deliver an easy to detect and obvious malware and your real payload to catch those convinced that they got it all.
This is the reason why being equipped for automatic reimaging of a server and quick rotation of keys and passwords should be standard practice nowadays.
You have now revealed that if somebody were to get access to one of your servers, they just need to drop some script kiddie trash at the very front, and then put their heavy stuff deep into the system.
You'll clean up the script kiddie trash, and call it a day.
This is the reason why being equipped for automatic reimaging of a server and quick rotation of keys and passwords should be standard practice nowadays.