It was an issue with table-deepcopy, but not due to it being missing, but because of lua metatable attached to that output table.
Factorio deepcopy routine checks if table has __self key to avoid copying API object references, and metatable attached there returned __self=0, which is why that table wasn't copied properly.
And copying is needed there, as it's a part of combinator state and should be present/updated in save files, unlike most other metatable-heavy stuff in mlc_env, which can all just be re-initialized on game load (maybe desyncing multiplayer, but oh well).
Should be fixed in 0.0.46+.
EDIT:
Oh, also, I think this bug have been there since the very first versions of this mod.
But it might be a bit hard to notice, as on game save/load, these tables get de-linked (initialized as separate ones, or maybe due to re-init of metatables).