You aint the only one; freaked me out too. Especially when Vera got sucked in and turned into a Cyborg.
And,
about a year or so ago I found out that it freaked out one of my friends also, even moreso.
Somehow I remember distinctively covering my eyes and refusing to watch the Vera/Cyborg scene. I think I was 4 or 5 when they aired the ABC extended version (my first time watching S3), but that scene freaked me out. Glad I'm not the only one.