One more tip for how to debug this kind of thing....

After you set $guess (whether you read it from STDIN or not), but before the line

if ($guess eq $correct[$i])
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you can see what the value of $guess is by doing

print "[$guess]";
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Note the square brackets ( [ and ] ). They are important here because they show where the value starts and ends. So if the value of $guess is Yellow\n, you get

[Yellow
]
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and you see clearly that you have a \n at the end (which you may not want).