Primary Problem
"...any of the buttons the value flickers(blinks) for a second then reverts to an empty input." 
The code provided from OP has form controls wrapped in a <div> rather than a <form> tag. The following demo presents a more accurate layout since it was mentioned:
"The html is all enclosed in form tags btw"
Problem
A <button> tag behaves as a submit button when it is nested within a <form> tag. So what happens is whenever a button is clicked, it is interpreted as a "submit" event and the <form> tag data is sent to a server if configured to do so, and if not configured, it will be attempted regardless. Each submit, failed or successful incurs the <form> to be reset. 
Solution
In order to prevent this reset, add this to each <button> tag:
type="button" 
Possible Problem
Because of the OP code being somewhat error prone and a bit inaccurate, there may be some misinterpretations. Upon initial inspection of OP code, the plus + button was concating values rather than incrementing a number. 
Plus Button Clicked 3 times
Result: 0111 
Expected: 3
Note: If the minus - button is clicked after clicking the + button without refreshing the code, it will function properly as expected, which is decrementing the value as a real number. But if clicked when the <input> has a value of 0, it does nothing.
Explination
Any value derived from a form control (e.g. <input>, <select>, etc.) is a string not a real number. So when 3 clicks of a plus button gives you this:
0111 
That's a string value concat from 4 strings:
"0" + "1" + "1" + "1" 
Solution
The string value must be converted to a real number value. There are many solutions already presented by other answers posted for this question, so I will just suggest what already implemented in the Demo below:
Instead of using: value +=1 and value -=1
Use this in/decrementing operators: value++ and value--
Under many circumstances, +=1 can be misinterpreted as:
 (this is a string) `value` (so concat) `+` (this string to it) `"=1"`
Whereas this operator: value++ has no ambiguities because it auto typed to a real number:
 (this is a string) `value` (***But*** convert it to a number) `++` (and add it to the default value of number 1)  
 The string value: "=1" would normally concat to =1 literally but since the OP code is using <input type='number'>, only numbers (in the form of a string) remain while non-number types are removed. Hence: 0111 instead of 0=1=1=1 value for the <input type='number' value='0'>
Details on JavaScript Data Types and specifically ++ and --
Demo
$(function() {
  $("#plus").click(function() {
    var pages_val = $('#pages').val();
    if (pages_val < 0) {
      pages_val = 0;
    } else {
      pages_val++;
    }
    $('#pages').val(pages_val);
  });
  $("#minus").click(function() {
    var pages_val = $('#pages').val();
    if (pages_val <= 0) {
      pages_val = 0;
    } else {
      pages_val--;
    }
    $('#pages').val(pages_val);
  });
});
<form>
  <button id="minus" type='button'>-</button>
  <input id="pages" name="pages" type="number" value="0">
  <button id="plus" type='button'>+</button>
</form>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>