Came across this line:
$body = RegEx::replace('...(some).*?(regex)...', '\\1\\2', $body);
Which got replaced with:
$body = \MyPhpScoperPrefix\RegEx::replace('...(some).*?(regex)...', '\MyPhpScoperPrefix\\1\\2', $body);
I worked around this issue by adding this to my scoper.inc.php:
'exclude-namespaces' => [
...
'1'
],
But it is of course a bug.