Yes, the values were grabbed from a file. How will that prind statement show newlines?
Well, if you enclose the values in single quotes, and there is a newline in the value, you'll see the ending quote on a line by itself.
I have alread checked the values in the file.
Checked them for what? If you've got like one filename per line, and you are reading them in with something like my @dependantFiles = <FH>; then each value in @dependantFiles will be terminated by a newline. You might just try calling chomp(@dependantFiles) before the code you posted. That may be all you need. (Although, you could stand to make some other improvements.)
Would it make a difference if I made the string I'm searching in seperated via commas?
No. Given the code you gave us, it doesn't matter what is separating the values in your $X strings. You aren't doing anything with the separating character or even with the separate values. You are simply treating it as one string.
"My two cents aren't worth a dime.";