I haven't seen this problem personally. there may be some unnecessary positioning code in the HTML/CSS/PHP that is involved with the code that you are trying to paste into Muse.
What would be needed to resolve your issue is the following:
1) a screenshot of your positioning in Muse' Design Mode.
2) a screen shot of the resulting position in Prieview or Publish.
3) the actual HTML code that you are pasting in.
Yes - I get that with some contact forms and facebook 'like' code. Hopefully this will be resolved with later versions with integrated forms.