Can you please show us a small, self-contained program that exhibits the problem so we can reproduce it? It should look something like the following:

#!perl -w
use strict;
use Net::SSH2;

my $local = '/home/test/test.txt';
my $remote = 'test.txt';
scp_put($local, $remote );
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(but that example doesn't write anything other than to a file named 'test.txt' for me). Did you maybe read the remote name from a file and did not clean up the line properly?