I just tried to use arcmap to create sample points (shp) and insert this shp as thematic layer. After doing that, I found the point dosen't match up. Which means that if I create a point on giant hogweed's flowers, the point's position changed in ecognition.

I've tried to open a clean Arcmap, and insert a vector map in GCS_OSGB_1936, and insert my drone data which is in GCS_WGS_1984. Then I reproject it by using Data Management Tools- Projections and Transformations- Raster- Project Raster and using "OSGB_1936_to_WGS_1984_7".

Then I clip the reprojected data to make sure background value is the same (I found some black lines or something else, which impacted the segmentation step).

Then I create a new shapefile-point data, and edit it to create 5 points which is on the flowers. However, when I open my drone data(reprojected and clipped) in eCognition and insert shapefile(5 points) as thematic layer, the position of these 5 points change a little bit, which cannot overlap the flowes.

I make sure they are both on OSGB_1936.