Wozniacki played despite recovering from a nagging calf injury and fell in a close match to Bencic 7-5 7-5 before indicating she felt pushed to play by the WTA rules.
"The rules, if you're a top-10 player are that this was my commitment tournament, you’re forced to play," Wozniacki told reporters.
"If you don't, you get huge money fines. You get zero points to your ranking ...which is crazy."
Wozniacki, a former world number one, was also defeated in the second round last week in Stanford as she battled injury.
Wozniacki was not alone in being upset in Toronto as third seed Petra Kvitova also went down, losing to former worlkd number one Victoria Azarenka 6-2 6-3.
Defending champion Agnieszka Radwanska avoided such a fate with her 7-5 6-3 triumph against Julia Goerges while second seed Simona Halep shook off the rust and stormed into the third round with a commanding 6-3 6-4 win over former world number one Jelena Jankovic.
Following a month off since her last competitive match, Halep looked sharp as she opened the North American hardcourt swing by reaching the third round in Canada for the first time.
The 23-year-old Romanian was in complete control on a blustery day, not allowing Jankovic a break chance in the opening set and then saving all three break points in the second.
Halep, winner of three tournaments this season including Indian Wells, broke her veteran Serb opponent to open the second set and that was all she needed to clinch a well-deserved win.
"I'm really happy I could win this match because I expected a tough match," said Halep, who has reached quarter-finals or better at eight of 11 tournaments this season. "I did a great game today.
"I didn't play a match since Wimbledon so I am really happy that I can say I played my best game."
Halep was joined in the third round by fifth seed Ana Ivanovic, a 6-4 7-6(4) winner over Belarusian qualifier Olga Govortsova, but it was otherwise a tough morning for seeds at the Aviva Tennis Centre.
Seventh seeded Czech Lucie Safarova was the big casualty, falling 4-6 7-5 7-5 to Russia's Daria Gavrilova.
After three consecutive first round exits, Gavrilova has enjoyed a superb run of form on the Canadian hard courts, beating former U.S. Open champion Sam Stosur in the first round before battling past French Open finalist Safarova.
Following Safarova to the exit were eighth seeded Spaniard Garbine Muguruza and Russian Ekaterina Makarova, the 11th seed.
Muguruza, playing her first event since reaching the Wimbledon final, slumped to a 7-5 6-1 loss against Ukrainian qualifier Lesia Tsurenko while Makarova, coming off a run to the semi-final in Washington last week, was tripped up by Slovenian qualifier Polona Hercog 6-2 6-7 (2) 7-5.
Italian 15th seed Sara Errani avoided adding her name to the list of surprises but only saw off American Madison Brengle in three tought sets 6-3 2-6 6-3.
(Reporting by Steve Keating in Toronto and Jahmal Corner in Los Angeles; Editing by Ian Chadband/Greg Stutchbury)
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