Nadal, who only recently returned from a stress fracture in the ribs, struggled badly at the back end of his match against the Canadian as he went down 1-6 7-5 6-2 in the last-16.
"I had my foot again with a lot of pain. I am a player living with an injury - it is nothing new. It's something that is there," Nadal, a 10-times champion in Rome, told reporters.
"Unfortunately, my day-by-day is difficult, honestly. Even like this, I am trying hard... it can be frustrating that a lot of days I can't practice the proper way."
The 35-year-old missed the bulk of last season due to the foot problem before mounting a remarkable comeback to win the Australian Open in January and also prevailing in Acapulco.
"Since I came back, the foot has been tough," added the Mallorcan. "Negative thing and toughest thing for me today is honestly I started to feel myself play much better. I started the match playing much better."
Nadal's preparation heading into the French Open, where he will be bidding for a record-extending 14th title, has been far from ideal after he was also knocked out of last week's Madrid Open by Carlos Alcaraz at the quarter-finals stage.
"First thing that I need to do is to don't have pain to practice... it's true that during the French Open, Roland Garros, I going to have my doctor there with me. That sometimes helps because you can do things," said Nadal.
"In the positive days and in the negative days, you need to stay and to value all the things that happened to me in a positive way."
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