I think you need to escape the quotes:
<?php echo do_shortcode('[gfchartsreports include="28" type="bar" chart_js_options="title: {display: true, text: \'Titletext\', fontSize:12,fontFamily:\'Arial\',fontColor:"#000",fontStyle:"bold",padding:20}" custom_search_criteria=\'{"status":"active","field_filters":{"0":{"key":"created_by","value":"current"}}}\']'); ?>