I am from Brazil and it is not unusual for companies to operate only within certain states because of this. Even though Brazil is a single country with a single language and mostly federal rules about things, there is still enough variance of laws from one state to another to cause problems.
Then you hear about Canada which has tariffs between its own provinces, but not to the US. Meaning some products are cheaper across the US border than across a province border. Figuring out how much to pay in taxes alone can be a blocker...
This is not an EU-only problem, any large single market will have friction in its internal divisions. It tends to be worse in the EU because the countries have a lot more sovereignty though (enforcement agencies tend to be local, not federal for example).