Sometimes a few source locations are dropped in forward computation so the stc gets out of sync with the original src. this means you need to call stc.project('pca', fwd['src']). It would be nice if you could use the original src.

This problem used to exist with stc.extract_label_time_course but that has been fixed maybe by #6789?

I'm not sure how to replicate this issue on sample data but I could share some data that exhibits the issue if that is needed.