I can think of two possible reasons that this is happening.
1. You are using a single quoted string:
$array = preg_split("/\n|,/", 'foo,bar\nbaz');
print_r($array);
Array
(
[0] => foo
[1] => bar\nbaz
)
If so, use double quotes " instead ...
$array = preg_split("/\n|,/", "foo,bar\nbaz");
print_r($array);
Array
(
[0] => foo
[1] => bar
[2] => baz
)
2. You have multiple newline sequences and I would recommend using \R if so. This matches any Unicode newline sequence that is in the ASCII range.
$array = preg_split('/\R|,/', "foo,bar\nbaz\r\nquz");
print_r($array);
Array
(
[0] => foo
[1] => bar
[2] => baz
[3] => quz
)