B::Deparse can shed some light . . .
$ perl -MO=Deparse,-p -e '$one_line =~ !/^#+/'
($one_line =~ (not /^#+/));
So what you were really doing was first matching /^#+/ against $_, taking the logical not of what that returned and then attempting to use the string version of that as a regexp to match against $one_line.
Update: And to further explain, that meant you were always splitting and hence would sometimes get lines without all the fields you expected and those would be undefined.
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