While using "r.stream.extract" make sure you are giving the correct settings which is as follows:
Input map : elevation map -- Use filled DEM
Minimum flow accumulation streams -- 1000 (or any of the desired value)
Advanced Parameters >> v.out.ogr output type -- select "line" from the drop-down
Save files unique stream ids (raster) and unique stream ids (vector) in the same location.
Suggestion: Keep trying with different accumulation values to get the correct stream network.