1. Inadequate Documentation
Regardless of whether you are applying to confirm your existing birthright citizenship, or are a permanent resident who now qualifies to become a Canadian citizen, if your paperwork isn't up to snuff, Immigration, Refugees & Citizenship Canadan (IRCC) is going to reject your application. The IRCC has no tolerance for "almost" getting it right.
You need to answer all the IRCC's questions in exactly the correct way, complete every last detail of every form, use the absolutely most up to date forms (they change frequently), and include all the required supporting documents. If the IRCC asks for additional information by a certain date, you need to provide them exactly what they are looking for by that day, or it's too bad, so sad.
To confirm birthright citizenship, while there are a number of required documents, there is some flexibility if those documents don't exist. But you first need to be able to prove you have looked for the requested documents, and cannot find any record of them. Next, you must present compelling proof in the absence of those documents, composed of a series of interlinked document.
2. You missed THE days of residency requirement
There's always been a days of residence in Canada requirement to qualify for converting permanent residency to citizenship. But back in the day, no one seemed to really keep track of how many days permanent residents were spending in Canada prior to their making citizenship applications, so this wasn't a hotly contested issue. Things are different now.
Not only does IRCC regularly interrogate would be citizenship applicants with demands for every airline ticket and passport stamp to their name since their original landing in Canada in order to verify just how many days were spent here, they even yank permanent residence cards at Canadian airports upon determining that there aren't enough days left to meet the permanent residency requirement, even sometimes years before the expiry of the PR card!
Revocation by the IRCC of your permanent residency based on insufficient days of residency can be contested before the Immigration Appeal Division (IAD) of the Immigration and Refugee Board (IRB). An adverse decision there can be further contested by seeking leave to bring a judicial review before the Federal Court.
If days of residency issues arise during you actual application for citizenship, IRCC may initially demand that you fill out a detailed residency questionnaire. Thereafter, you case might be referred to a Citizenship Judge within the Citizenship Commission which is an internal administrative body within the IRCC and not part of the IRB. Citizenship Judge findings can be contested by seeking leave to bring a judicial review application to the Federal Court. Be aware that even if you win before a Citizenship Judge, the Minister could challenge that decision before the Federal Court, just as you could challenge a loss.
3. You made a misrepresentation to IRCC
The IRCC gets very touchy about what they call "misrepresentations." The problem is that even an innocent accidental single mistake in filling out a form can be held to be a misrepresentation, leading to a finding of inadmissibility and denial of an application.
You will usually get a chance to make additional submissions to the IRCC on why it really wasn't a misrepresentation prior to the IRCC making a final decision on your case if they believe a misrepresentation has occurred, but you might nonetheless need to proceed before the Federal Court to contest a reject. You need to be very, very careful in interpreting every question asked on a citizenship application not just in a grammatical sense, but in the sense that the IRCC intended (which can be difficult to figure out). Some questions even require you to apply Canadian law to foreign legal situations. Thus retaining legal counsel to assist with your citizenship application may be well justified.