Scribal convention versus scribal error Brian van Norden's book Classical Chinese for Everyone says 


  We have learned from ancient manuscripts discovered in excavated tombs
  that it was once extremely common for scribes to substitute
  homophonous characters for one another. (page xx)


I believe this was an accepted practice.  On the other hand, human reality tells us some of it was just by mistake. 
 
Do experts today have any good idea how much of it was deliberate and accepted, versus how much was by mistake?   For example, there is good evidence that some European manuscripts were copied by scribes who really did not understand the material they were copying --  and those scribes made plain mistakes.  Do experts have a good idea how often that happened in China?

Have experts today identified systematic rules that ancient scribes might have followed, saying which homophone substitutions are acceptable or even preferable?
Experts know. Some homophone substitutions are very common and widely accepted and they have a name "通假字". If you want to understand Classical Chinese, you'll have to know these common 通假字s. And of course plain mistakes also exist. If you read enough, you'll know which are acceptable and which are just mistakes.