It is not expected behaviour.
The box knows the difference between regional channels and even on boxes with both terrestrial and satellite tuners it knows the difference between channels of the same name on, say, Freesat and Freeview.
If the box is set or recording from BBC TWO NI HD it suggests that you selected that regional channel when setting up the autotimer (or when you modified it to include more channels to search)
I wonder if you have two types of filter set up?
When you go to menu/timers/autotimers click on your MOTD autotimer
Then press blue (new)
If
Editing = Channels
you may see something like ...
auto1.jpg
Now change
Editing = Bouquets
You should see no Bouquets listed as shown below
auto2.jpg
If however you have a bouquet listed as shown below
auto3.jpg
The autotimer may(?) check all the channels configured on "Editing = Channels" AND all the channels in the "Sky UK - HD" bouquet which will include all the regional variations
(Bouquet = a list of channels)
If a bouquet is listed try deleting it and just leave your list of channels. You will have to save the changes AND when in the top list of all Autotimers press green again to save the fact you have made a change to one item in the list of autotimers.
All the channel names and bouquet in the screen shot examples above are on my box, the regional channel selections and bouquet name(s) on your box may be different.
By the way, you may also like to include the RB RB1 HD (red button channel) in your list of channels as that sometimes includes alternative MOTD football matches