She probably applied under the family route using form SET(M) which will fail. That is because the family rules require 60 months under the family rules, where as the skilled worker rules simply need the dependant partner to have been just a
dependant for 5 years regardless of the route she is under.
She should have applied using form SET(O) as dependant of skilled worker. So her applying using form SET(O) under the correct route should succeed now without any issues. The fact that you have ILR is also not an issue as you settled under the skilled worker rules.
Dependant Partners qualifying period
Dependant partners of Global Talent, Innovator Founder, T2 Minister of Religion,
International Sportsperson, Scale-up and Skilled Worker lead applicants must
complete a 5-year qualifying period before they qualify for settlement.
If the lead applicant has settlement on the basis of long residence (including where
they have subsequently naturalised as British citizens) provided they held leave
under the relevant PBS route at the time when they settled, their partner can extend
their permission or gain settlement as a dependant under these routes.
If the partner has switched into the partner of a settled person category they can
apply for settlement without having to switch back to the relevant route. For more
information relating to partner of settled person see Appendix FM guidance.
Where the lead applicant has been granted British citizenship, their dependants can
still apply if they held permission as dependants at the time.
If the lead applicant is being granted settlement in, gained settlement through or has
been granted citizenship following, UK Ancestry or Representative of an Overseas
Business permission, the dependant may apply for settlement without completing a
qualifying period and provided they can switch into the route.
5-year permission requirement: partners
Those who are required to complete a qualifying period must have spent a
continuous period of 5 years in the UK with permission as a dependant partner of the
lead applicant.
Dependant partner can include time as a spouse on family routes.
https://assets.publishing.service.gov.u ... routes.pdf
Advice is given based on my personal research and experience only. Do NOT contact me via private message for immigration advice