How to set an image height & width on a video in ffmpeg
You can add a scale filter. This will scale the image to 50x50:

ffmpeg -i in.mkv -i 3.png -filter_complex "[1]scale=50:50[b];[0][b] overlay=25:25:enable='between(t,0,20)'" -pix_fmt yuv420p -c:a copy tout.mkv pause


If you want to scale the width or height and maintain the aspect ratio, use -1. For example, this scales the width to 50 and the height according to the aspect ratio. 

scale=50:-1


Conversely, this scales the height to 50 and the width is adjusted by aspect ratio.

scale=-1:50