The whole passport validity question can get a bit tricky as each case is quite specific. The normal reason for the duration of 90 days is in case something happens and you are unable to return home due to illness or quarantine such as may happen during this Pandemic.
As your wife holds a Spanish passport, it has to be valid for when she returns to the UK. Please take a look at the UK government website on Entering the UK
for some information.
Just to be on the safe side, has she tried to fast track her passport renewal, maybe the Spanish Embassy
could advise too?