There is a real potential problem when using back-to-back tickets with "partner" airlines, particularly if you apply the frequent flyer miles to a single program.
The practice of back-to-back ticketing is prohibited in the Contract of Carriage regardless of who the carrier is.
Obviously if you travel on different carriers it's pretty difficult for them to catch you, but if you are traveling on the same airline's planes and crediting the miles to the same account it's a different story.
snake recommends that you request a copy of the Contract of Carriage from both carriers to read when you are waiting for delayed flights, or when you are having trouble sleeping at night. It might be useful to prepare for the possibility of a call from the Revenue Protection Unit.