functions.php

<?php

/**
 * This is an (arguably messy) setup to test what might be a hook issue.
 *
 * Jchristopher_Hook_ID_Test_Alpha stores an array of strings to prepend to the_content.
 * It has a hook jchristopher_test allowing for other code to modify the array of strings.
 * It has its own string 'alpha'.
 *
 * Jchristopher_Hook_ID_Test_Beta has its own string 'beta' and uses the hook from the
 * first class to append 'beta' to the list of strings to prepend to the_content.
 *
 * Jchristopher_Hook_ID_Test_Gamma also has its own string 'gamma' which it also
 * adds to the array of strings using the jchristopher_test filter.
 *
 * Lastly there is a closure that also aims to append it's own string 'closure' to the
 * array of strings that is prepended to the_content.
 *
 * Problem: The remove_filter call in Jchristopher_Hook_ID_Test_Beta->add_string()
 * removes the closure which has a higher priority, and it's never executed.
 *
 * Expected output: 'alpha beta gamma closure' prepended to the_content
 * Actual output:   'alpha beta gamma' prepended to the_content
 */

class Jchristopher_Hook_ID_Test_Alpha {
	private $strings = [ 'alpha' ];

	function __construct() {
		$this->run();

		add_filter( 'the_content', function( $content ) {
			return implode( ' ', $this->strings ) . ' ' . $content;
		} );
	}

	function run() {
		$this->strings = array_merge( $this->strings, array_filter(
			apply_filters( 'jchristopher_test', [], $this ),
			function( $string ) {
				return is_string( $string );
			}
		) );
	}
}

class Jchristopher_Hook_ID_Test_Beta {
	private $strings = [ 'beta' ];

	function __construct() {
		add_action( 'init', [ $this, 'run' ] );
	}

	function run() {
		add_filter( 'jchristopher_test', [ $this, 'strings' ], 20 );

		new Jchristopher_Hook_ID_Test_Alpha();
	}

	function strings( $strings ) {
		remove_filter( 'jchristopher_test', [ $this, 'strings' ], 20 );

		return array_merge( $this->strings, $strings );
	}
}

new Jchristopher_Hook_ID_Test_Beta();

class Jchristopher_Hook_ID_Test_Gamma {

	function __construct() {
		add_filter( 'jchristopher_test', [ $this, 'strings' ] );
	}

	function strings( $strings ) {
		return array_merge( ['gamma'], $strings );
	}
}

new Jchristopher_Hook_ID_Test_Gamma();

// This closure is not executed unless the priority is reduced below 20
// which is the priority of the hook removed in Jchristopher_Hook_ID_Test_Beta->strings()
add_filter( 'jchristopher_test', function( $strings ) {
	$strings[] = 'closure';

	return $strings;
}, 21 );

Here are the IDs during the call to remove_filter:

Turns out it's a logged issue https://core.trac.wordpress.org/ticket/40393