Make sure that you are loading both the bootstrap-toggle js file and css file properly. Specifically check that they are in the location your links point to, or even use the cdn versions listed below:
<link href="https://gitcdn.github.io/bootstrap-toggle/2.2.0/css/bootstrap-toggle.min.css" rel="stylesheet">
<script src="https://gitcdn.github.io/bootstrap-toggle/2.2.0/js/bootstrap-toggle.min.js"></script>
Your paths must be wrong or you forgot to include the js file altogether, and you should see a warning about this in your console because otherwise the code works fine.
Regarding dynamically loaded content.
The first elements work because, after the html first loads, bootstrap-toggle.min.js looks for any elements that have the attribute data-toggle="toggle" and calls .bootstrapToggle() on them applying the plugin. This only happens when the page loads.
If you later add more toggles, you'll need to initialize them yourself via .bootstrapToggle(). Iv'e updated the example below to simulate adding toggles dynamically and explain the approach I would take to do that. See the comments in the code for more details.
// timeout to simulate ajax
setTimeout(function(){
// add an element dynamically,
$('.table').append('<tr><td>Testswitch0</td><td><label><input type="checkbox" data-toggle="toggle" data-onstyle="success" id="S2" data-size="mini"></label></td></tr>');
// now that we have dynamically loaded elements
// we need to initialize any toggles that were added
// you shouldn't re-initialize any toggles already present
// but we also do want to have to figure out how to find the ones we added
// instead, we'll destroy all toggles and recreate all new ones
$("[data-toggle='toggle']").bootstrapToggle('destroy')
$("[data-toggle='toggle']").bootstrapToggle();
}, 2000)
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
<link href="https://gitcdn.github.io/bootstrap-toggle/2.2.0/css/bootstrap-toggle.min.css" rel="stylesheet">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script>
<script src="https://gitcdn.github.io/bootstrap-toggle/2.2.0/js/bootstrap-toggle.min.js"></script>
<div class="panel panel-primary" id="switchespanel">
<div class="panel-heading">
<h3 class="panel-title">Switches</h3>
</div>
<div class="panel-body">
<table class="table">
<tr>
<th>Location</th>
<th>State</th>
</tr>
<tr>
<td>Testswitch0</td>
<td><label>
<input type="checkbox" data-toggle="toggle" data-onstyle="success" id="S0" data-size="mini">
</label></td>
</tr>
<tr>
<td>Testswitch0</td>
<td><label>
<input type="checkbox" data-toggle="toggle" data-onstyle="success" id="S1" data-size="mini">
</label></td>
</tr>
</table>
</div>
</div>
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