Nulls (\0, ASCII character 0) are commonly represented by the sequence ^@ by many *NIX tools. While it's unlikely you've set $/ so that chomp would get it chop certainly would if it was the last character of the string.

$ perl -le '$x = qq{abc\0}; print $x; chop $x; print $x;' | od -xa
0000000      6261    0063    610a    6362    000a                     
+   
           a   b   c nul  nl   a   b   c  nl
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Of course were there more context or (even better) actual code shown someone might be able to make more than that kind of vague guess. (See How (Not) To Ask A Question)

Update: Added sample.