I would definitely write in as that seems like a bit of an unpolished way this was handled but the status based meal priority extends only to VIP and SE (upgrade vs cash vs aeroplan doesn’t matter) so they technically weren’t entitled to any priority on meal choice. A good crew will often extend meal priority to other elites after giving first choice to SE but they don’t have to. Additionally I think in the terms of eupgrades they stipulate that they can get away without giving you a meal because it’s an upgrade so no meal is guaranteed the FA might have taken that as the license to take away meal choice but a different FA could have easily gone the other way and chosen the lowest status person to get the short end of the stick (but arguably that would be less in the spirit of getting a meal on an upgrade isn’t guaranteed). Either way I would write in if nothing else they might send a discount code for doing so.