I spent a fair bit of time looking into this a few years back. I was travelling on an Australian passport and entered and exited the EU quite regularly so I had built up quite a collection of stamps to the point where my passport was almost full. Often upon leaving the EU the border agent would start looking at all the stamps then shrug their shoulders, one time a trainee just looked up at his supervisor who must have said "don't worry about it", but once (in Germany) the border guard got out a calculator and added up every single stamp and gave me a stern lecture for being close to the 90 day limit and that I should never go over it.

It was explained to me that the different countries' systems are not linked so for that reason they rely upon the physical stamps to calculate your compliance. Somebody mentioned if crossing a border without a stamp you could call into the next police station and they could provide some proof of exit.

Bottom line - do worry about it and just keep some proof (eg your exiting boarding pass) for your next entry to the EU.