Found a quick review:

I'm running a 12 speed cassette with no issues. Check your lower limit screw and also try fine tuning in the app. I have my ER9 tuned using gear protection and optimal shifting for climbing in my small chainring. Though I can shift big/big and small/small no issue.

Also check that your derailleur hanger is aligned properly and that your cassette is seated properly in the freehub. I've noticed 12 speed is a bit more finicky so any little thing out of adjustment can affect shifting.

Worst case scenario is reset all settings using the app and start fresh. Make sure to double check if your RD is properly screwed into the derailleur hanger. Good luck!

It's not a limit issue that I can tell but I will double check. When I back out the screw it will over shift outboard. I can adjust the trim on the 12 cog to go over to the 11 and it will stay there, but it will not shift to the 11 and stay,  I do not have gear protection turned on and it is doing the same in both chainrings up front.  Next stop is the factory reset and redoing the 6th gear calibration.  Or swap back to the 11 speed cassette.  Yes, I use 12 speed chains on all my bikes.

Issues with 12 speed cassettes.  I am having a problem getting it to shift into the last 11 tooth cog on two different wheelsets.  I have backed off the limit screw so much that it has over-shifted on the outboard side so I don't think the limit screw is the problem.  It will actually shift to the 11 and then about 2 seconds later it shifts back up to the 12.  if i hold the button down, it will stay in the 11 but as soon as I release the shift button, it shifts back to the 12.  I did replace the wonky looking narrow/wide type pulley with one from a 6800 ultegra derailleur I had laying around.  That helped shifting all over but the 11 cog is a mystery.  When I use an 11 speed wheel and change it to 11 speed in the settings, it has no issue shifting the entire range.

I'm running a 12 speed cassette with no issues. Check your lower limit screw and also try fine tuning in the app. I have my ER9 tuned using gear protection and optimal shifting for climbing in my small chainring. Though I can shift big/big and small/small no issue.

Also check that your derailleur hanger is aligned properly and that your cassette is seated properly in the freehub. I've noticed 12 speed is a bit more finicky so any little thing out of adjustment can affect shifting.

Worst case scenario is reset all settings using the app and start fresh. Make sure to double check if your RD is properly screwed into the derailleur hanger. Good luck!

Issues with 12 speed cassettes.  I am having a problem getting it to shift into the last 11 tooth cog on two different wheelsets.  I have backed off the limit screw so much that it has over-shifted on the outboard side so I don't think the limit screw is the problem.  It will actually shift to the 11 and then about 2 seconds later it shifts back up to the 12.  if i hold the button down, it will stay in the 11 but as soon as I release the shift button, it shifts back to the 12.  I did replace the wonky looking narrow/wide type pulley with one from a 6800 ultegra derailleur I had laying around.  That helped shifting all over but the 11 cog is a mystery.  When I use an 11 speed wheel and change it to 11 speed in the settings, it has no issue shifting the entire range.

Which front chainring are you in while you're attempting this? Is it, perhaps, trying to prevent cross-chaining and shifting to the same ratio but with a different front chainring?

I believe I read a post where someone was pulling their hair out over their Wheeltop electronic derailleur doing something like this before realizing it was a feature not a bug.

Issues with 12 speed cassettes.  I am having a problem getting it to shift into the last 11 tooth cog on two different wheelsets.  I have backed off the limit screw so much that it has over-shifted on the outboard side so I don't think the limit screw is the problem.  It will actually shift to the 11 and then about 2 seconds later it shifts back up to the 12.  if i hold the button down, it will stay in the 11 but as soon as I release the shift button, it shifts back to the 12.  I did replace the wonky looking narrow/wide type pulley with one from a 6800 ultegra derailleur I had laying around.  That helped shifting all over but the 11 cog is a mystery.  When I use an 11 speed wheel and change it to 11 speed in the settings, it has no issue shifting the entire range.