It is entirely correct to feel bad when using "was" the way it is in the example given:
Das ist das Thema von gestern mit dem Word/PDF-Extrahieren, was bei dem Kunden nicht 100 % funktioniert.
The grammar may be correct but still this sentence does not say clearly what is meant by "was". The relative pronoun "was" references the subject of the preceding clause, and that could also be "Thema" like:
Yesterday's subject on extracting documents does not work.
This of course does not make any sense. Therefore people may still understand it in a colloquial setting. In other sentences it may work the other way round:
Das ist das Leid mit dem Verstehen einer Sprache, was ich sogar nachvollziehen kann.
Note that this example is not good style either, because we do not really know what is being understood here.
If you want to be clear it may be better to keep the diction simple by not using relative clauses:
- Das ist das gestrige Thema über das bei dem Kunden nicht 100 % funktionierende Word/PDF-Extrahieren.