Outside Windows you only get a subset of the ecosystem, so you always have to watch out for libraries that have been written or ported to .NET Core explicitly, as a large majority of them might work on .NET Core on Windows, but fail everywhere else due to what they are using from Windows/COM.
Additionally there are 15 years of .NET Framework ecosystem that can't be easily migrated to .NET Core due to breaking changes.
Java doesn't suffer from this problem.