I ran into the same problem a while back.
My solution was to change the AxisMapStrategy to OAMS_TRADITION_GIS_ORDER.

You can read more about this here:
https://gdal.org/tutorials/osr_api_tut.html

My code in C#:

            var source = new SpatialReference("");
            var destination = new SpatialReference("");
            Geometry ogrGeom = null;
            CoordinateTransformation transform = null;

        //set spatialrefrence for source and destinaton epsg
                source.ImportFromEPSG(sourceEPSG);
                destination.ImportFromEPSG(destEPSG);
                    
          
source.SetAxisMappingStrategy(AxisMappingStrategy.OAMS_TRADITIONAL_GIS_ORDER);
                 
destination.SetAxisMappingStrategy(AxisMappingStrategy.OAMS_TRADITIONAL_GIS_ORDER);

                //create coordinate transformation with source and destination 
spatialreference
                transform = new CoordinateTransformation(source, destination);

                //create a gdal geometry object from Wkt and transform it
                ogrGeom = Geometry.CreateFromWkt(geom.Value);

                ogrGeom.Transform(transform);
                //export transformed geometry
                ogrGeom.ExportToWkt(out string outGeom);

-------------------------------------------------------------------------------------------------

-----Ursprüngliche Nachricht-----
Von: gdal-dev <[email protected]> Im Auftrag von Even Rouault
Gesendet: Dienstag, 28. Januar 2020 17:12
An: [email protected]
Betreff: Re: [gdal-dev] Transform produces different results from 2.2.4 and 
3.0.2 or 3.0.3

> What might I need to do to get it working correctly? I know there was 
> a lot of changes with gdalbarn/proj.

Indeed. See
https://lists.osgeo.org/pipermail/gdal-dev/2020-January/051425.html

--
Spatialys - Geospatial professional services http://www.spatialys.com 
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