So, recently in one of the game opponent decided to reduce my order pool via command token, but not 2 ordersfrom 1 Combat group, but an order from group 1 and 1 order from group two. I've looked this in the rules, but there is not specified, that it has to be from 1 group. So is it correct?
Eye-lifting, indeed. Your opponent was correct, the orders can be removed from more than one group up to a total of 2, note the plural on "groups" in the copy-paste from the rules below; The player using the Command Token will decide from which Combat Group or Groups the nullified Orders will come from.
Yes, it appears so. You can reduce the order pool. Each order pool is defined by 1 combat group. http://infinitythewiki.com/en/Order_Pool The rule also goes to state the following: "Nullify two Regular Orders of the enemy Order Pool during that Turn only. The player using the Command Token will decide from which Combat Group or Groups the nullified Orders will come from. The player can only perform this option in the enemy Tactical Phase, after the Order Count." So the rule actually specifies that not only can you reduce two orders from an order pool, you can are free to choose how those orders are distributed.
