What was your status before you became a PR?
This is quite common for people who were visitors prior to getting their PR, and there have been many reports of this in the forum, if you want to search.
People who had work and study permit usually don't get this problem as IRCC can easily validate their records in this case.
As for how to "solve" it, well, the only ironclad method is "nevermind, I'll withdraw and reapply once I accumate enough days as a PR and don't need to rely on these days".
If you don't want to abandon the current application, you can simply answer that you're sure of your calculation, and provide as much proof as you can to justify every single day of physical presence : flight tickets, rental or property proof, bank statements, work or studies proof if you had these statuses in Canada, or even stuff like Google Maps history or social media activity proving the presence in Canada. The more the better I guess. What's for sure : the onus is on you to prove the physical presence, so better be convincing.
Also, please note that if you go this route, it may (may, not necessarily will!) take ages, many months and potentially years, before IRCC makes a decision, and there is no guarantee the decision will go your way. If you still live in Canada and have accumulated enough days since you applied to be either eligible without pre-PR days or relatively close to it, or if you keep the current application going but the physical presence stays in progress by the time you reach 1095 days as PR, I would advise you to go with a fresh application. There's a good chance going back to the starting block gets you to the finish line faster.
Obviously up to you, depending on your circonstances, the physical presence proof you're able to present to IRCC, whether you still live here or left since you applied, and, frankly, your risk tolerance regarding a potential delay or even dismissal of your application if the above proof is deemed inconclusive or incomplete. Good luck.
