IBM WebSphere employs a method of class caching for performance reasons, loading bytecode into a cache persisted on disk that can be shared by mutliple applications using the same JDK.
Because the APM Java Agent performs bytecode instrumentation, references to the Java Agent code are also stored in this cache
When updating the Java Agent version, the cached version of the agent's code may have been changed.
This can lead to conflicts causing problems with both the agent's and monitored application's behaviour.
The recommendation would be to clear the WebSphere class cache after every change to the agent code, particularly where upgrading the version, but also advisable where applying individual fixes
IBM information on clearing WebSphere class caches: