Well its happened to me twice, I put the codeshare'd flight number (ie: AC4084) instead of the actual flight number (ie: UA939), and the Customs dude went into a typical line of "let's shake out this liar" round of questioning, until realizing that I had arrived on a UA flight, but had written down the AC codeshare number.

There's nothing illegal or dishonest about it -- but a Customs officer doesn't get a manifest for an AC flight, an LH flight, a CO flight, a SK flight, etc., etc., when an UA flight arrives in Canada. He gets an UA manifest, with a list of UA passengers that are 'of interest' (ie: previous infractions, arriving from at-risk origins), and has to work off of that.