Probably because you used split with an expression that were empty or contained only newlines \n here:

@split_hit_non_barrel=split(/\n/, $separate_hit_non_barrel);
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Since split absorbs its seperators, it would then return an empty list.
The first entry of an empty array would give an undef value:

$hit_line_non_barrel=$split_hit_non_barrel[0];
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Using an undef value for a match would give a warning then:

$hit_line_non_barrel=~/^(.*?)\s+/
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This is just guessing, using the Perl debugger would be much better. You can even customize the debugger, so it stops right at the point when the warnings occurs -> Re: Debugging a program and Re^3: Debugging a program allowing you to look what has gone wrong while having the whole context available. I am using this regularly with my code.