I don't have messages of errors or warning. But running GeoGebra (5.0.367.0 18 June 2017 Java 1.8.0_131-64bit) with 3D graph doesn't work.
I don't why 3D doesn't work.
I added java@FreeBSD.org - I hope there is a Java-expert who has an idea.
I have been using this software for months but this was the first time I wanted to use the 3D functions.
I do not know java, I can not help on this point, by cons I can always test. For example, here is a file exported from GeoGebra online that does not open with the FreeBSD version.
Created attachment 185085 [details]
Test for geogebra 3D
Simple test (a pyramid) from geogebra online