Helen’s Eidolon, you’re not the only one. I, too, remembered it as Through a Scanner Darkly. It’s mentioned here and on multiple sites. Mass hallucination? Too much D?
“Through a Glass, Darkly” and/or “In a Glass Darkly” has been reasonably popular for titles for both fiction and non-fiction for decades. For example, I recall an Agatha Christie short story with that title that was from the 20s or 30s (I read it in the 80s just to be clear); and there was a novel in the 80s by someone called Karleen Koen that I believe was on the bestseller list. I did a search on Amazon.com for “glass darkly” and it returned 175 results.
I’ve always thought of it as one of those poetic/Biblical references that seems to turn up as a handy allusion in book titles.