This is not a bug. '=' has special meaning in ?= and ?<= expressions and it is on 
the list of characters quotes by preg_quote.

"=" will be quoted to "\=", in this case, the result is R\=1 R\="3" R\="5" too, whenever "\=" or "\\=".

$search = array(
	'/required/',
	'/min\=(\d+)/',
	'/max\=(\d+)/',
	'/\w+\=([^=]+)/',
);
$replace2 = array(
	'R=1',
	'R="$1"',
	'R="$1"',
);
in this case, the result is still ="3" =code

This is happening because of the fourth search expression /\w+\=([^=]+)/. It matches the previous replacements and removes them. Without it, this:

echo preg_replace(
	array('/required/', '/min\=(\d+)/', '/max\=(\d+)/'),
	array('R=1', 'R="$1"', 'R="$1"'),
	'required min=3 max=5 code=code'
) . "\n";

Outputs:

R=1 R="3" R="5" code=code

(As expected.) But the replacements happen one after the other instead of simultaneously, so then it will do the equivalent of this:

echo preg_replace(
	'/\w+\=([^=]+)/',
	'',
	'R=1 R="3" R="5" code=code'
) . "\n";

..which will match and remove 'R=1 R' and 'R="5" code', producing the "puzzling" output:

="3" =code

Here is one way to solve it, by doing all the matches simultaneously with one regexp:

echo preg_replace_callback(
	'/(\w+)(?:=(\S+))?/',
	function ($parts) {
		if (!empty($parts[2])) { // have '='
			if ($parts[1] == 'min' || $parts[1] == 'max') {
				return 'R="' . $parts[2] . '"';
			} else {
				return '';
			}
		} else {
			if ($parts[1] == 'required') {
				return 'R=1';
			} else {
				return $parts[0]; // unmodified
			}
		}
	},
	'required min=3 max=5 code=code'
) . "\n";

This outputs:

R=1 R="3" R="5"

Thank you very much!