The Agility Editor will sometimes have difficulty recognizing the formatting that you add to your content, especially if that content was originally copied from another source.
The failsafe way to get back on track to clear our all HTML formatting:
Click on the 'Format Stripper' button
Choose 'Strip All Formatting'
This will clear out all formatting in your content and you can start again from scratch.
Note that you can try stripping out the CSS, Word, Span and other formatting using the Format Stripper tool before resorting to this.