Happened to me a lot after alters started gaining the confidence and trust to interact with the therapist, which I believe took a few months before I started noticing it. I found it to be quite frustrating but ultimately it turned out to be a positive sign and opened the doors for some leaps in progress.

Something I eventually realized in retrospect is that some of my alters had solid reasoning to challenge the therapist, based on their perceptions.

1. Therapist was a woman in a position perceived as superior, which reminded some alters of my mother.
2. Therapist asked questions for which the answers were considered secrets for various reasons.
3. Therapist figured out the existence of the alters, which in and of itself was a huge secret, and one that was taken rather than willingly given away in the perceptions of some alters.
4. Therapist tried to reassure and gain trust, which some alters (especially one in particular) had learned was a warning sign of malice to come.

In other words some protectors were just doing their jobs. Many of my experiences losing time or getting very foggy-minded in therapy turned out to be protectors testing, gauging and challenging the therapist. This was a necessary process.