I have generated 2 times the same orthomosaic, one with WebODM and another one with a different software.
The point is that I can’t crop the WebODMmosaic in QGIS using Raster/Extraction/Cutting Raster by mask layer, but it work perfectly with the raster generated with other software.
Where’s your PNGW? You’re going to need both the raster and the vector to be properly georeferenced, with the appropriate georeference files (prj for SHP, PNGW for PNG), or use a format that supports this natively (GeoTIFF).
You’re also working in global EPSG:4326 instead of the local UTM CRS WebODM should have selected for you.