A not-so-difficult approach is to create a few tie classes, for arrays, scalars, hashes, and even filehandles if you wish. The classes should either log, or carp whenever a tied variable is modified.
You won't be tieing every variable in your script (probably), but you can easily tie a few important (or suspect) ones.
I posted a node with example code for tieing a scalar for the purpose of watching its access here: Re: Trapping acces to variables in-code. The example can easily be used as a starting point for hashes and arrays too.
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