I tried it like this -
data:text/html,<script src="data:text/javascript,var a = 0;%250d%250aa++;%250d%250aconsole.log(a);"></script>
It only happens for me if I select the entire expression and hover over it (and that behavior is expected - the Developer Tools feature runs the selected expression as if it were run by the page and returns its value. Side effects can happen and the JavaScript state is affected as usual). Otherwise, it only shows the value of a.
What version of Chrome are you using and on which platform?