Without showing what exactly's in $MAKECOMMAND people are only going to be guessing, but your problems in your command that's getting passed to the shell not your perl. You may have a trailing semicolon, or another | on the end of it, or who knows what.

Another aid in debugging is to build what you're passing to system in a scalar and print that scalar's contents out so you know exactly what you're giving to the shell.

my $cmd = "$MAKECOMMAND | tee ...";
print STDERR "cmd: !!$cmd!!\n" if $DEBUGGING;
my $ret = system( $cmd );
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