For example: if you have a field that uses an interface (eg Address) and it returns a concrete type (eg EmailAddress) but that type is not explicitly referred to elsewhere (as a return type or parameter) then the SpecificationLoader will never see it. Hence, if that class gets used (eg an EmailAddress is retrieved from persistent memory) then an exception will occur.
The best long term solution is to load all classes from the Jar(s) that contain the DOM code. This could be indicated by placing a marker, such as a file, in the metadata.of the Jar.
In the meantime a simple workaround is to add a method, typically to a service, that uses the concrete class and mark it as hidden. Give the method a name that makes it clear what the method is there for so nobody tries to use it.