When there is movement, you can use either word. You can say either 'Put the stones in these holes' or 'Put the stones into these holes'. The sentence with 'into' gives more of an idea of the action of inserting the stones into the holes, but you could equally well say 'in', and the meaning would be the same. In this context, the two are interchangeable. If there is no movement, you can only use 'in'. For example 'Where are the stones?' 'They are in the holes'.

Both prepositions are actually used in a correct way.