It's hard to say without any code, but try this after you instantiate your Map object:
map.infoWindow.fillSymbol = new SimpleFillSymbol(SimpleFillSymbol.STYLE_NULL);
That overrides the highlight symbol used when a feature is clicked.
Here's a complete example:
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="viewport" content="initial-scale=1, maximum-scale=1,user-scalable=no"/>
<title>Disable Highlighting</title>
<link rel="stylesheet" href="http://js.arcgis.com/3.14/esri/css/esri.css">
<style>
html, body, #map {
height: 100%;
width: 100%;
margin: 0;
padding: 0;
}
body {
background-color: #FFF;
overflow: hidden;
font-family: "Trebuchet MS";
}
</style>
<script src="http://js.arcgis.com/3.14/"></script>
<script>
var map;
var featureLayer;
require(["esri/map", "esri/layers/FeatureLayer", "esri/InfoTemplate",
"esri/symbols/SimpleFillSymbol", "esri/symbols/SimpleLineSymbol", "esri/Color",
"dojo/domReady!"],
function(Map, FeatureLayer, InfoTemplate,
SimpleFillSymbol, SimpleLineSymbol, Color) {
map = new Map("map", {
basemap: "topo",
center: [-122.45, 37.75],
zoom: 4
});
featureLayer = new FeatureLayer("http://services.arcgis.com/P3ePLMYs2RVChkJx/ArcGIS/rest/services/CDC_Weekly_Flu_Surveillance_Map/FeatureServer/0", {
infoTemplate: new InfoTemplate()
});
//The following line overrides the highlight symbol used when a feature is clicked.
map.infoWindow.fillSymbol = new SimpleFillSymbol(SimpleFillSymbol.STYLE_NULL);
map.addLayer(featureLayer);
});
</script>
</head>
<body>
<div id="map"></div>
</body>
</html>