Shortcode appearing outside content

It sounds like that shortcode is executing and echoing, rather than executing and returning.

Shortcodes don’t echo, they are supposed to return a string variable for instance.

Incorrect

function my_shortcode($atts) {
  echo "string";
  ?>Hello World<?php
}

Correct

function my_shortcode($atts) {
  $content = "string";
  $content .= "Hello World";
  return $content;
}

Now that said im not familiar with the plugin you referenced but likely your php function isnt returning as above, and the plugin simply executes the function which echoes to the head when we preload the modals in the head to check for other plugins shortcodes to make them compatible like Gravity Forms.