I've always supported Janeway in all her decisions (Tuvix included) and I think she always had sound judgement and knew how to impose her authority, she's a brilliant captain.
However, the one time I disagreed with her was in the episode "Prey". In that episode she proved to be stubborn and let her personal differences with a crew member (7/9) cloud her judgement. Furthermore, she tried to please both the 8472 and the Hirogen, I think the expression kill two birds with the same stone (or something of the sort) was used at some point during the epidose, can't remember exactly, but this is the one time when i thought Janeway was a fool and 7/9's assessment of the situation was realistic and sound.
Janeway almost got everyone killed - good to see 7/9 take the initiative and save the day. With the exception of this single episode I always admired Janeway for her decisions and her command of the ship, but her stubbornness in "Prey" disappointed me.