I'm trying to georeference a TIFF file in QGIS (version 3.20.0-Odense) based on a WMS layer (EPSG:4326). The project is in EPSG: 25832 and I used the same as output for the georeferencing (4 points, Helmert, nearest neighbour). The georeferencing runs without any errors, but the TIFF finally ends up in a wrong position miles south.
Georeferencing in a complete new project with all (project, WMS and output) in EPSG:4326 leads to the result down:
The red points at the top left corner are my target point on the WMS layer, the TIFF south east of it and way too large.
Warp (reproject)
to project it into EPSG: 25832 before loading it into your original project. There is also this question that raises the issue of rasters appearing in the wrong location after a QGIS update.