Is there any flexibility on the 90 days in the last 12 months at time of applying for citizenship? The wording says 'should' which gave me a little hope.
On the UK gov website it's says - "You should not have: spent more than 450 days outside the UK during the 5 years before your application. Or spent more than 90 days outside the UK in the last 12 months."
There's no deadline for applying for citizenship... you just apply whenever you meet all the requirements. That could be the day you receive ILR (if you meet the requirements now), or it might be in 2 years' time (if you have to wait to meet the requirements).
The 12-month period is rolling, so all she has to do is not apply for UK citizenship until she is back below 90 days out of the country in the last 12 months.
What dates were you out of the country?
Also, for people married to UK citizens, the residency period is only 3 years, not 5 years.
The residency requirements for your wife will be:
- she must hold ILR
- she must have been inside the UK exactly 3 years prior to the date she submits the citizenship application
- she must not have been outside the UK for more than 270 days in the last 3 years, with no more than 90 of those days being in the last 12 months before applying (you don't count the day you left or the day you returned to the UK.
There is a little bit of leniency with the days outside the UK. They will normally disregard up to 300 days in the last 3 years, and up to 100 days in the last 12 months (see here:
https://www.gov.uk/government/publications/form-an-guidance/form-an-guidance-accessible#bookmark11)