Add your code here: http://bootply.com/66598
The image below shows your problem / question (I think): 
To understand your problem, you will have to examine the grid and understand the difference between the default grid and the fluid grid, see http://twitter.imtqy.com/bootstrap/scaffolding.html#gridSystem
Your problem will occur on screens larger than 767 pixels. Below the width of the columns (div with class = "span {x}") will drain. On large screens, the problem also fails.
Default Grid (Twitter Bootstrap 2.x) :
When nesting lines, the child line gets the full range, which is summed up to the span of its parent.
Example:
<div class="row"> <div class="span6"> <div class="row"> <div class="span3"></div> <div class="span3"></div> </div> </div> <div class="span6"> </div> </div>
In a grid, span classes have a fixed width in pixels (depending on the width of the screen), see
Screen width 768px and 980px: Each span1 will be 940 - (11 gutters 20px) / 12 = 60px (above 980px (1170-11 * 30) / 12 = 70px).
Now your problem you have set is: <input type="text" class="input-medium search-query"> As an input environment, this input will have a fixed width of 150 pixels and the Search button also takes up space (75px;) . You put this in span2 ( <div class="input-append span2"> ), the witch in gap 3 ( <div class="span3 offset9"> ). In the default 940 grid, the span3 range got a width of 3x60 + 2x20 = 220px; while your seachbox takes 75 + 150 = 225 pixels. For this reason, your Iskander comes out of the grid. This problem will not have span4. Of course, this is also Span2.
Fluid Mesh (Twitter Bootstrap 2.x and Twitters Bootstrap 3) :
In a liquid grid, each column (span {x}) receives a percentage of its parent's width. When nesting a child row can be divided into 12 columns.
Example:
<div class="row-fluid"> <div class="span6"> <div class="row"> <div class="span6">50% of the parent and 25% of the grid</div> <div class="span6">50% of the parent and 25% of the grid</div> </div> </div> <div class="span6"> <div class="row"> <div class="span12">100% of the parent and 50% of the grid</div> </div> </div> </div>
In your case, your search box is nested in span2 in span3. Span 3 will receive about 25% of the grid width. When 25% of your grid width is less than 225px, the search box will exit the grid. So your problem will start with a screen width of 4 x 225 = 900 pixels (just below the default grid of 940 pixels). Also here it will help put your search query in the range of 4 or 5. NOTE <div class="input-append span2"> will have a width of 16.6% from 25% (very small).
Possible Solution. Use the pull-right class for the search query :
<div class="row-fluid"> <div class="span3 offset9"> <form class="form-search"> <div class="input-append pull-right"> <input type="text" class="input-medium search-query"> <button type="submit" class="btn btn-info"><i class="icon-search icon-white"></i> Search </button> </div> </form> </div> </div>