**i raised a similar protractor issue on this , the issue seems like**

 1. if you give a input say "**one**" to textbox 'A' 
 2. then you clear text box 'A'
 3. and then sends **input** to textbox 'B'
 4. and then sends input say "**two**" again to textbox 'A', A will get the value **onetwo**

**If you immediately use sendKeys after using clear() , everything works fine.**

 1. if you give an input say "**one**" to textbox 'A'  
 2. then you clear text box 'A'
 3. and then sends input say "**two**" again to textbox 'A', A will get the value **two**

In my case using the element in order fixed the issue

link to issue:

https://github.com/angular/protractor/issues/5370