Pode ser que o filterdiff não saiba como lidar com a opção git, já que seu PATTERN parece ok:
$ mkdir a b
$ seq 5 > a/file1
$ rm file1
rm: remove regular file ‘file1’? y
$ seq 5 > b/file2
$ seq 4 > b/file1
$ seq 4 > a/file2
$ diff -r -u a b
diff -r -u a/file1 b/file1
--- a/file1 2015-03-07 09:24:15.548744157 +0100
+++ b/file1 2015-03-07 09:24:37.804744069 +0100
@@ -2,4 +2,3 @@
2
3
4
-5
diff -r -u a/file2 b/file2
--- a/file2 2015-03-07 09:24:42.448744051 +0100
+++ b/file2 2015-03-07 09:24:30.684744097 +0100
@@ -2,3 +2,4 @@
2
3
4
+5
$ diff -r -u a b > my.patch
$ wc my.patch
16 46 302 my.patch
$ filterdiff --exclude='*/file2' my.patch | wc
9 28 178
$ filterdiff --exclude='*/file2' my.patch
diff -r -u a/file1 b/file1
--- a/file1 2015-03-07 09:24:15.548744157 +0100
+++ b/file1 2015-03-07 09:24:37.804744069 +0100
@@ -2,4 +2,3 @@
2
3
4
-5
diff -r -u a/file2 b/file2