CKeditor automatically wraps lists

I use CKeditor for my CMS. However, this CMS uses custom variables to display values and apply some logic. An example would be:

<ul>
    <li>one</li>
    [[if (val==true)]]
    <li>two<li>
    [[endif]]
    <li>three</li>
<ul>

However when I save this HTML source my CKeditor automatically wraps my logic in in li-tags like this:

<ul>
    <li>one</li>
    <li>[[if (val==true)]]</li>
    <li>two<li>
    <li>[[endif]]</li>
    <li>three</li>
<ul>

I read the docs of course and tried a whole bunch of configs, however this auto-wrapping seems to be unable to disable. Help would be greatly appreciated