I had not heard of this issue before, but it does not surprise me. There are several known issues involving cantrips gained from other sources than the "main" spell selection interface. Off the top of my head, I can also name:
A Forest Gnome gets Minor Illusion from their racial background. A School of Illusion Wizard gets Minor Illusion from their subclass, or gets a different cantrip of their choice if they already have Minor Illusion. When a Forest Gnome becomes a School of Illusion Wizard, they do not get another cantrip of their choice, but instead get Minor Illusion listed twice on their character sheet.
The Telekinetic feat grants access to the Mage Hand cantrip, or instead doubles the cantrip's range if the character already knows Mage Hand. The character app does not recognize this interaction.
Unfortunately, cantrips in general are and always have been pretty buggy on the site, and I feel safe saying that the issue you've described is unlikely to be fixed any time soon. Given how many of these seemingly-related issues go completely unacknowledged, I don't feel there's any evidence the devs even care.
ETA: looool, as of this moment, the topic right below this one in this forum is an issue (albeit not a cantrip-related one) that was marked as being a "Bug" nearly six years ago and still has not been fixed. And while of course I cannot see the backend, that one does not seem like it would be especially hard to fix either - since in theory it would involve nothing beyond adding a few options to a dropdown menu, with no other mechanical interactions. If the devs can't be arsed to even do that (or if their backend is so spaghettified that they can't even edit text without breaking things), then yeah. I'm afraid the odds of bugs like these cantrip issues ever being addressed, seem close to nil.
Pact of the Tome grants access to cantrips from any spells list, but they all count as warlock spells
Rod of the Pact Keeper increases Warlock Spell's Spell Attack and Saving Throw by +1
Pact of the Tome Cantrips are not granted this increase on character sheets, despite being warlock spells
(At least in the example I've seen, which was sapping sting)
I had not heard of this issue before, but it does not surprise me. There are several known issues involving cantrips gained from other sources than the "main" spell selection interface. Off the top of my head, I can also name:
These issues have existed for a long time. The first one I listed has been around since at least early 2019 without being fixed. As far as I know, the devs have failed to even acknowledge most of these issues in any official capacity.
Unfortunately, cantrips in general are and always have been pretty buggy on the site, and I feel safe saying that the issue you've described is unlikely to be fixed any time soon. Given how many of these seemingly-related issues go completely unacknowledged, I don't feel there's any evidence the devs even care.
ETA: looool, as of this moment, the topic right below this one in this forum is an issue (albeit not a cantrip-related one) that was marked as being a "Bug" nearly six years ago and still has not been fixed. And while of course I cannot see the backend, that one does not seem like it would be especially hard to fix either - since in theory it would involve nothing beyond adding a few options to a dropdown menu, with no other mechanical interactions. If the devs can't be arsed to even do that (or if their backend is so spaghettified that they can't even edit text without breaking things), then yeah. I'm afraid the odds of bugs like these cantrip issues ever being addressed, seem close to nil.