Forgive the naïve question but I thought when the boarder guard scans the passport before stamping that it should flag whether or not you've hit the 90 days? Or am I wrong? Only time I've been questioned on entry was in Berlin when I was asked how long I was planning on staying, as three weeks prior I'd left Malaga where the boarder guard didn't scan my passport and just stamped it there and then when I handed it over. I told the Berlin guard that and he just rolled his eyes and then stamped my passport.

I did visit ARN on a tier point run last year but it was via HEL. I wasn't asked anything on the transit through HEL (used e-gate and then the passport was stamped) but I do remember the boarder guard questioning me when going back through passport control at HEL. Think he was bemused at me transiting back after one day but I said I'd been in Stockholm and was summarily stamped out and it wasn't unfriendly or aggressive.

In any case the OP's partner was treated disgracefully and by the looks of it, illegally, by the ARN boarder force. If he had proof of onward travel I really don't see why they had any reason to refuse entry.