No, its a feature
As I understand your question you have:
1. A two-tank platoon-type formation
2. Two tanks, Tank1 and Tank2, same class both X-3 code and available
3. When you make the formation, you have Tank1 as a template in the first slot and Tank2 as a template in the second slot.
When you select the formation you want it to include one Tank1 and one Tank2.
AFAIK the game doesn't work that way. If the two tanks are the same class, it will always choose the same tank for the two slots in the formation and always choose the tank in the first slot.
That is one reason why we have a sh*t-load of different classes that are often simple clones of each other
If you want to make sure you get both tanks in your two-tank formation, make one a different class from the other. If you look in the game guide, you can check out the unit classes. As long as you use one that is labelled "tank clone", it doesn't have any special abilities but simply serve as a means to differentiate one tank from another.
If, for example, you make Tank1 unit class 102 and Tank2 unit class 103, you will get both tanks in the same formation always.
Btw. be sure to check the Game Guide and Mobhack guide about the problems of using the X3 radio code with template units!
Claus B