Gap in Irish residency when applying for citizenship

Has anyone heard of or experienced Irish Immigration showing leniency in exceeding the 90 days break in residency stamps. Will my application be rejected outright or is there a vehicle for arguing my circumstances?

The situation was
My stamp 4 visa expired in september 5th 2018 as my passport expired on that date.
The Brazilian embassy delayed to send me the new passport and I couldn't get an appointment with Immigration in Dublin.
The earliest appointment I managed to get was on 27th December 2018. I had been trying to get an appointment every day, but there was never any available. By the end of November I found out that you could buy appointments from third party company on facebook and that's how I managed to get one.

I am applying for Citizenship through marriage and hoping to prove 3 years of stamps. I am resident in the country 12 years.

Although you meet the residency requirement, a gap of more than 90 days between residency permissions is a very serious one. This basically means that you were living in the country illegaly and I would be more concerned about your status rather that the outcome of citizenship application.

However, as you've managed to get a renewal after getting a new passport, you might want to try to provide an explanation and a proof for the gap if you decide to apply.

If you've been resident for 12 years, for an ordinary application you need to show the last year continuous and four other years from the previous eight.

That shouldn't be a problem