It would seem that cards that are in both Caverns of Time and the Core Set only show their CoT versions in the current Twist format.
For example, Ship’s Chirurgron is in the current Core set and CoT, so only the Caverns version is available, and anyone with only the Core version can’t use it.
This is in contrast to a card like Crimson Clergy, where you can use either the Core Set or the Legacy version.
If you can use Core Crimson Clergy, that is the bug. Core is not one of the sets in this season’s Twist
Only Core cards that are also available from other sets are usable, not all Core cards.
That seems very bizarre to me. No Core cards should be usable if it’s not a valid set
i remember an old post where developers said they should be interchangeable so i think is a bug.
I suspect there are multiple already reported bugs in twist supporting this function , like collection fails to show if you have one copy in a set and another in the other set even if both are valid .
But i need to test it more
That post was about CoT
Like if CoT is not a valid set of a format, but Gadgetzan is, and you have the CoT version of Aya Blackpaw, then you can use that CoT version instead of the Gadgetzan version, even though CoT is not a legal set in that format.
Maybe it also applies to core set, or any other mixed sets 
Might as well update, the bannings of the Rumble crossover cards did not include a fix for this.