This happened to me with a program, as I had only uploaded an unofficial copy of my transcripts and my official copy hadn't been received. My application was also marked as incomplete, and I was vexed.
Contact the department first (by phone or e-mail), explain the situation, and provide your application ID. Meanwhile, try to get your official transcript in as soon as you are able. More than likely they will confirm that your transcripts aren't needed until admission.
The response I received from that graduate program coordinator was that my application was already being reviewed without the official transcripts and "That said, should you be offered admission, we will need an official transcript reflecting your Bachelor's degrees. This will need to be sent to [], and instructions can be found here []. As I said, though, this is not holding up or affecting the evaluation of your application." Pretty standard. So definitely don't worry, but also don't delay in contacting the program staff.