Flag variables are often a warning of using the wrong program structure.

On the other hand, I came across some convulted printing code :

if ( ..A... ) {
   if ( ..B.. ) {
       if ( ..C.. ) {
           if ( ..D.. ) {
               print .....
           } else {
               print ...
           }
        } else {
           if ( .. D2.. ) {

... you get the idea ...
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It took some effort to reverse engineer the original specs, but I was able to simplify it to:

my $flag1 = cond1;
my $prefix = (( cond2 ) ? "strting1" : "strring2";
...
print "$prefixA$suffixB" if ( condC );
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While things are spread out in the sense that things are detected and saved in flags in one spot, and used later, it avoids dealign with a highly nested conditional ( especially since some possible states were ignored.

Of course, there are other solutions to the problem I encountered, but that's not relevant tothe topic of flag variables.