diagnostic criteria for DID states -

"A. The presence of two or more distinct identities or personality states (each with its own relatively enduring pattern of perceiving, relating to, and thinking about the environment and self).

B. At least two of these identities or personality states recurrently take control of the person's behavior. " http://www.behavenet.com/capsules/disorders/did.htm

so my answer would be yes they can. regardless of what you are doing in therapy (or any thing else - sleeping eating, at school, at work, ...what ever) there is always the risk that an alter is going to take control and do what ever their job / purpose for being is. thats why they were created and are there for right. with me it didnt matter if I was in therapy, out on a date or just lounging around in the back yard. my alters took over when ever and where ever they needed to according to what their purposes and jobs were. thats what got me sent to a psychiatrist for testing, my alters were taking over when ever where ever and finally my therapist recognized my symptoms and sent me for testing.

have you considered talking with your treatment providers. they can explain in more detail about DID and how it affects your life and help you to control it.