Just a few thoughts...
1. Use strict
2. Use HTML::Template. It really cleans up your code
3. Not sure what you are trying to do here. (See ysth post)
@cut = $newObject->cut_seq($seqobj);

my @tables = ();
my $counter = 0;
foreach my $fileSeq (@sequences) {  # loop through all the sequences
  my $seqobj = Bio::PrimarySeq->new ( -seq => $fileSeq, -alphabet => '
+dna');  # create an object of the sequence

  foreach my $element (@enzymes) {  # look through all the enzymes for
+ each sequence
    my $newEnzyme = new Bio::Tools::RestrictionEnzyme(-NAME => $elemen
+t);
    push @tables,{
      COUNTER => $counter++,
      CUTSEQ => $newEnzyme->site(),
      ELEMENT => $element,
      ANNOTATE => $newEnzyme->annotate_seq($seqobj),
      CUT => $newEnzyme->cut_seq($seqobj),  ##### ???? ######
    };
  }
}

.. and in .tmpl file
<TMPL_LOOP NAME=TABLES>
<TABLE BORDER=2>
<TR><TD><B>Sequence number <TMPL_VAR NAME=COUNTER></B></TD></TR> <!-- 
+FIX </tr></td> here -->
<TR><TD>The cleavage site is <TMPL_VAR NAME=CUTSEQ> for enzyme <TMPL_V
+AR NAME=ELEMENT> denoted by " ^ "<BR></TD></TR>
<TR><TD>
  The annotated sequence is given below along with the digested sequen
+ce<BR>
  <B>Annotated:</B><TMPL_VAR NAME=ANNOTATE><BR>
  <B>Digested:</B<TMPL_VAR NAME=CUT>
</TD></TR>
</TABLE><BR><BR>
</TMPL_LOOP>
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