Board Thread:General Discussion/@comment-28128661-20160404143233/@comment-5956954-20160418060903

Mabian wrote:

There may be a hint that Alphys is aware of Flowey as a sort of malevolent talking flower or something along those lines, since she seems rather shocked when Papyrus mentions that a talking flower told him to gather everyone. I can guess Alphys was shocked because it was probably the flower that left the room when she checked. Could guess she was mildly shocked but might also be in question that it was a "talking flower." the Question Mark was there. Might've been rhetorical, though.

In short, the malevolence was unexpected, but the sentience was known.