There is no limit on number of days outside the UK when you are on FLR(M)... and even if there was (as there is for work visas), it would be 180 days, not 90.
The important thing for FLR(M) is that you and your wife have lived TOGETHER for the entire length of the visa, whether that's in the UK or abroad... so if you both travel overseas together and live together for the entire time, it won't affect the FLR(M) at all (as long as you can show you were living with each other overseas).
However, where it can be tricky is if your wife travels overseas alone and you stay in the UK, because you are not then living together for that period.
They can overlook it if you have very good reasons for not being able to live together though, such as military deployment, being sent overseas for work by your UK employer, or other compelling, unavoidable reasons... and you can prove your relationship was subsisting while you were apart.
The only limits on days outside the UK are for UK citizenship after 5+ years in the UK, where you have to show no more than 270 days outside the UK in the last 3 years before applying for citizenship, with no more than 90 of those 270 days being in the last 12 months before applying.