This can happen. A few years ago I obtained a 5 year Brazilian visa. I entered Brazil within 90 days of the visa's issue, but at that time the authorities at GIG were for some reason not stamping passports. I noticed that no one got a stamp upon either entry or exit.

The next time I went to Brazil I was a bit worried that the lack of proof of use in the passport might cause a problem, so I took with me a hotel receipt from Rio showing that I had been in Brazil during the 90 day period. The gate agent at American noticed the lack of an entry stamp. I expalined what had happend. She then called the consulate in Los Angeles, but they didn't know anything. Finally she said: "I hope this all works out" and gave me a boarding pass. On arrival at GIG they stamped my passport and admitted me to the country.

I assumed that meant that everything was OK for future trips since my passport now proved that I had been allowed to enter Brazil. My next trip created no problems. But when I went again the following year the gate agent almost refused to let me on the plane. Finally she agreed to talk to her supervisor. They let me board the plane, but told me that the airline had been fined by Brazil for letting me travel the previous occasion. (If that was really true I am not sure why they let me travel.)

Before my next trip to Brazil I obtained a new visa. Anyone who gets a 5 year visa for Brazil and thinks there is any possibility that they might want to go to Brazil again in that 5 year period should make sure that the Brazilian authorities stamp the passport.