my $wordcnt='Bob|Tom|Dave|Tom|Bob|Dave';

What is the significance of the repetition of words in $wordcnt? Repeated patterns in a regex alternation have no effect. The regexes /Bob|Tom|Dave/ and /Bob|Tom|Dave|Tom|Bob|Dave/ and /Bob|Tom|Dave|Tom|Bob|Dave|Dave|Tom|Bob|Dave|Bob/ are equivalent.

... the code also gives a total word count ...

I don't see how the posted code does this.

... MATCH the wordcnt with the FIELD in the flat file.

This implies that each word being searched for occurs only once in a line from the flatfile (or maybe in the the entire flatfile). Is this true?

Update: There are no boundary assertions in the OPed pattern, so 'TomTom' will count 'Tom' twice. Is this what you want?