I don't know if anyone else is having this issue??
I've upgraded to 2.0.1 and now - occasionally - I will highlight a word(s) then click on a clip from the clips toolbar (different clips have the same issue) and the clip will paste into the replace field of the find/replace window. Once it gets in this mode I close and re-open Sigil and it works fine.
I haven't figured out
exact replaceable steps
What I have been doing is a lot of find/replace before this happens. I have no idea if that is a factor.