is there a way to fix it?
No, skipping to the new content considers all previous events that are required before the Fourth Act to be completed as passed. Therefore, the last conversation event with Mikasa is also completed. However, you can play through all previous content before it. I think I'll make it so that skipping to the new content will unlock all the actions with Mikasa and Asuna, not just the last event. Thanks for bringing this to my attention.