Schengen Visa delivered by France and Proof of Accommodation, but difficulties traveling within Schengen area

My Thai girlfriend has a Schengen Visa with multiple entries delivered by France, with a Proof of Accommodation (Attestation d'Accueil) with my family in France. We made a side trip to Portugal and flew back from Lisbon to Basel-Mulhouse airport. There was control at Basel-Mulhouse by the French immigration police control (although France, Portugal, and even Switzerland are all Schengen countries).

The police stated that the Proof of Accommodation was not valid anymore as my girlfriend had traveled outside of France, and held us up for 1/2 an hour. Fortunately, maybe, my girlfriend had entered Schengen initially via Vienna and the Austrian police had not stamped the Proof of Accommodation (ignored by them because it was a French document?). So the French police at Basel-Mulhouse put a stamp on the document and eventually allowed my girlfriend into France.

This raises questions. Although we had made similar trips around Schengen countries several times before with no issue whatsoever, there is clearly a risk.

Imagine the hypothetical situation as follows:

• A foreigner has a Schengen Visa issued by France, and is accommodated by a family in France:
• that family says "let's go for a weekend to Amsterdam (or Berlin, or Rome or wherever else within Schengen);
• there is a police control at the border coming back from that weekend to Amsterdam (or etc etc);
• the police declares that the Proof of Accommodation document has already been stamped when entering France at the start of the visit, and therefore is not valid anymore;
• the foreigner is not allowed to return to France.

Would that not be totally ridiculous and completely against the well-known principle that with a Schengen visa, one is allowed to travel freely within all Schengen countries?