My concern is not about length of stay initially,but this could impact at a later date,when or if the 90 days were exceeded. I have spoken with several couples,who don’t have,the luxury on of one of them having an Irish passport,who have knowingly exceeded the 90 day rule,and had no comeback. I have not heard of anyone personally that has been,stopped or challenged about their plus 90 days in Europe. Has anyone (directly) and not rumours!
My parents, one with an EU passport and the other not, routinely stayed in France for four months every summer for several years. They once caused a slight commotion by going through passport control separately, after which they always went together.
EU law is clear on the matter: the non-EU spouse is a "person enjoying freedom of movement under union law" as defined in the Schengen Borders Code when the couple are traveling together, and is therefore entitled to use the "EU passports" queue. As you have noticed, however, some border officers have a policy that does not comply with the law.
Another point on which the law is clear is that the other queue is not a "non-EU" queue but rather an "all passports" queue that EU citizens are also entitled to use. Therefore, if they tell the non-EU spouse not to use the EU queue, the couple should be able to stay together because the EU spouse should be able to go to the "all passports" queue. (If the staff object, I would try pointing out that the sign says "all passports.")
In any event, even if the staff at the border checkpoint require the couple to go through separately, it has no effect on the legality of staying longer than 90 days. The fact that the non-EU spouse has a derived right of free movement stems from the circumstances and does not depend on which desk or which officer processed the entry. It should suffice to show the facts:
- one person is an EU citizen
- the two people are married
- the two people were traveling together
In my experience (and that of my parents) it has never been necessary to show this formally; a simple "this is my spouse" has always been enough.
when we have gone through passport control, both in the UK and Spain, we have tried to explain this to the passport officials, who in the main seem oblivious to the rules. On most trips we have been guided through the EU and non-EU terminals, separately, and my spouse's passport has been stamped.
The Schengen Borders Code specifies that the non-EU spouse's passport should be stamped in these circumstances (i.e., she does not have a residence permit) so you're unlikely to be able to avoid that. The presence of the stamp does not change the fact that your wife enjoys freedom of movement.
Also none of this affects anything to do with UK border control. Even when the UK was in the EU their practices were different, because the UK had opted out of the Schengen area; the Schengen Borders Code did not apply. They don't call the non-privileged queue "all passports," for example, but rather "other passports." I always took my non-EU partner to the EU queue and was told that I shouldn't have, whereupon they processed us together anyway.
As for Spain, you could try printing out the Schengen Borders Code and circling the relevant definitions, but it's a bit convoluted and you're not likely to get the message across in an airport setting. As mentioned above, the second option would be to try going together to "all passports," and the fallback is to go through separately. Your wife's passport is going to get stamped no matter what, and she is covered by free movement rights regardless.