You don't show how you open the file, and you don't tell us the platform you're using.
If you are on Windows, my guess is that you forgot to use binmode on the file, and newline translation is hitting you.
If that guess is wrong, then please show a short, self-contained program that reproduces the problem, and also tell us the version of Perl you're using.
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Want more info? How to link or
or How to display code and escape characters
are good places to start.