You misunderstand the use of refining.
you purify p88 you should have p93. Jasmins explanation of p88 was that it was a rough synthesis and p93 was a stricter lab procedure to return a purer yield of that molecule. P88 was said to have active impurities as a result of this rough synthesis. If its an impurity its in such a small amount along with who knows what other impurities active or inactive are in there.
What you should really be asking is why dont they identify that “impurity” and make it.
The problem with the rough synthesis as explained by jasmin is that its not always repeatable.