Having worked on the inside: this is by design. You know for 100% that Pepsico and Coca Cola unleashed an army of lobbyists to make sure the laws were written in a way where the single market only worked for large business.
I'm surprised that was necessary. A single look at the EU website leaves no doubt that the EU is perfectly capable to create a bureaucratic nightmare all by itself (and incapable not to even if it tried).
Lobbyists don't do this. Regulators/lawmakers need to be corrupt and/or incompetent for lobbying to do this.
It's comforting to believe that large corporations with the greed of the rich and powerful is what makes these inefficiencies but really it's about a million little political negotiations, primarily driven by voters dislike of change.