The message "instrumentation disabled because not all transformations could be completed" basically means that the agent could not finish instrumenting all the classes in due time. This can be attributed to several issues. Most commonly, however, there could be network connectivity issues between the agent and collector - this can be checked in the agent log (please verify log entries from System Information dashlet). Additionally, depending on the state of the collector host and monitored application hosts (i.e. VMware environment) there could be packet loss issues contributing to this behaviour. See https://kb.vmware.com/kb/2039495, https://kb.vmware.com/kb/1010071, or https://kb.vmware.com/kb/2056468, for more info.
Finally, the cause might be excessive processing on the collector side through instrumentation of huge amounts of classes, as it is known with some 3rd party assemblies. Known are already certain 3rd party assemblies from vendors like Aspose or DevExpress, which can cause an in general non-critical disconnect, but in case immediately afterwards one essential assembly is tried to be instrumented, the disconnected state will likely trigger the same problem. Those assemblies can - like other non-essential assemblies - be excluded from instrumentation following this KB article: How to exclude assemblies from instrumentation
The consequence is that no sensors can be placed on classes within those excluded assemblies anymore, but due to obfuscation, the class and method names might not be of interest in a PurePath anyways, but autosensors will still bring visibility into non-instrumented assemblies. Additional benefit of excluding assemblies will be some memory overhead improvement (depending on assembly size).
This issue has also been discussed here:
Hope this helps.