Create a script that create another script

Doing It Right

If the content you want to insert is hardcoded, use a quoted heredoc:

# Because of the quotes around EOF, nothing inside this heredoc is modified.
cat >test.sh <<'EOF'
stock=banana/
touch "$stock/file"
EOF

If it's not hardcoded, then an unquoted heredoc becomes appropriate -- but requires some care:

#!/bin/bash
#      ^^^^-- /bin/sh does not support any means of eval-safe quoting
#             ...a ksh derivative such as bash will provide printf %q

stock=banana/                    # Presumably this is coming from a generic source, ie. $1
printf -v stock_q '%q' "$stock"  # Generate an eval-safe quoted version of stock

# Because the sigil is not quoted, expansions inside the heredoc are performed unless
# they're escaped.
cat >test.sh <<EOF
stock=$stock_q
touch "\$stock/file"
EOF

Note that we're using printf %q to generate a safely-escaped version of the value and inserting that (in an unquoted context) into the generated script; and being sure to escape all expansions which are intended to be performed by the child shell (thus replacing $stock with \$stock).

Answering The "Why"

Your "$stock" was expanded by the original shell, before it was passed to echo.