diff --git a/lib/libalpm/conflict.c b/lib/libalpm/conflict.c
index c093705a..3442902c 100644
--- a/lib/libalpm/conflict.c
+++ b/lib/libalpm/conflict.c
@@ -251,10 +251,7 @@ static alpm_list_t *chk_filedifference(alpm_list_t *filesA, alpm_list_t *filesB)
 	alpm_list_t *ret = NULL;
 	alpm_list_t *pA = filesA, *pB = filesB;
 
-	if(pB == NULL) {
-		return(alpm_list_strdup(pA));
-	}
-
+	/* if both filesA and filesB have entries, do this loop */
 	while(pA && pB) {
 		const char *strA = pA->data;
 		const char *strB = pB->data;
@@ -279,6 +276,15 @@ static alpm_list_t *chk_filedifference(alpm_list_t *filesA, alpm_list_t *filesB)
 			}
 	  }
 	}
+	/* ensure we have completely emptied pA */
+	while(pA) {
+		const char *strA = pA->data;
+		/* skip directories */
+		if(strA[strlen(strA)-1] != '/') {
+			ret = alpm_list_add(ret, strdup(strA));
+		}
+		pA = pA->next;
+	}
 
 	return(ret);
 }
diff --git a/pactest/tests/upgrade011.py b/pactest/tests/upgrade011.py
new file mode 100644
index 00000000..d8ed8734
--- /dev/null
+++ b/pactest/tests/upgrade011.py
@@ -0,0 +1,16 @@
+self.description = "Upgrade a package with a filesystem conflict"
+
+p = pmpkg("dummy", "2.0-1")
+p.files = ["bin/dummy", "usr/share/file"]
+self.addpkg(p)
+
+lp = pmpkg("dummy", "1.0-1")
+lp.files = ["bin/dummy"]
+self.addpkg2db("local", lp)
+
+self.filesystem = ["usr/share/file"]
+
+self.args = "-U %s" % p.filename()
+
+self.addrule("PACMAN_RETCODE=1")
+self.addrule("PKG_VERSION=dummy|1.0-1")