You have said he was admitted in the basis of the
immigration rules as a "visitor" one day after being refused entry as a long term migrant under the
EEA free movement rules. You have also said that the border officer was aware of the earlier refusal.
I think several mistakes were made by home office.
First of all the initial EEA refusal was clearly incorrect. As pointed out in the court case mentioned, there is not a time limit to the SS rights (and you are also not required to stay in a particular location for SS rights to remain). You can appeal and I suggest you do that.
The successful entry was made under EU free movement law, because the spouse was covered by EU free movement law (because of SS). This is true even without any intention or explicit action on the part of the border guard.
The officer might have also done an admission on the basis of the immigration rules. Or the officer might have been vague in describing the entry and it was actually done on the basis of EU free movement laws.
I tend to think the the description was vague, and then entry was actually on the basis of EU free movement law. Typically if you have been refused entry as a long term settler, then it is very unlikely that they will (the next day!) let you in as a (immigration rules) visitor: they will obviously suspect (maybe with good reason) that you will try to stay. There is no different under the EU free movement rules between entry for a short visit and long term residence.
Anyways, you are in the UK. Welcome!
I would suggest you do a SAR to get the details from your home office file:
http://www.ukba.homeoffice.gov.uk/navig ... onal-data/ It takes 40 (business?) days to get a reply.
If you are worried about your status, I suggest you consult with a solicitor who really understands EU free movement law.