Likely you should retain the '$' character in the command line, so escape it, by preceding it with a backslash. Otherwise, perl will fill in the value of the variable $(.

$x = `grep orderNumber \$(find /home/homedepot/ECOM/prod/in -mtime -1)
+ | wc -l`;
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Alternatively, use the qx with single quotes:

$x = qx'grep orderNumber $(find /home/homedepot/ECOM/prod/in -mtime -1
+) | wc -l';
[download]