When copying a directory with scp on macOS, the placement of the trailing slash matters.
If you want to copy the folder source and keep the folder itself in the destination path, use:
scp -r /path/to/source user@host:/path/for/dest/That will copy the source directory into /path/for/dest/.
For example, if you run:
scp -r /Users/martyn/source user@example.com:/tmp/the result on the remote host will be:
/tmp/source