How to user the Tablediff Utility with Replication Filters
Run TableDiff.exe against a view configured to limit the source table in the same way your replication filter does.  I've created an example here:

USE Test;

    /* Create two test tables, TableDiff1 is the source and TableDiff2 is the destination */
CREATE TABLE TableDiff1
(
    TableID INT NOT NULL CONSTRAINT PK_TableDiff1 PRIMARY KEY CLUSTERED IDENTITY(1,1)
    , FilterColumn INT NOT NULL
    , TableData NVARCHAR(255) CONSTRAINT DF_TableDiff1_TableData DEFAULT (NEWID())
);

CREATE TABLE TableDiff2
(
    TableID INT NOT NULL CONSTRAINT PK_TableDiff2 PRIMARY KEY CLUSTERED IDENTITY(1,1)
    , FilterColumn INT NOT NULL
    , TableData NVARCHAR(255) CONSTRAINT DF_TableDiff2_TableData DEFAULT (NEWID())
);


    /* Create some dummy data in TableDiff1 */
INSERT INTO TableDiff1 (FilterColumn, TableData) VALUES (1, DEFAULT);
INSERT INTO TableDiff1 (FilterColumn, TableData) VALUES (1, DEFAULT);
INSERT INTO TableDiff1 (FilterColumn, TableData) VALUES (2, DEFAULT);


    /* Copy the dummy data into TableDiff2, with a FILTER */
INSERT INTO TableDiff2 (FilterColumn, TableData)
SELECT FilterColumn, TableData
FROM TableDiff1
WHERE TableDiff1.FilterColumn = 1;

    /* Add some more data to TableDiff1 that does not exist in TableDiff2
       so TableDiff.exe shows differences between the two tables */
INSERT INTO TableDiff1 (FilterColumn, TableData) VALUES (1, DEFAULT);

SELECT * FROM TableDiff1;
SELECT * FROM TableDiff2;




Next, we run TableDiff.exe against both tables, clearly there will be differences since we are not excluding the filtered rows (FilterColumn = 1)


  C:\Program Files\Microsoft SQL Server\110\COM>TableDiff -sourceserver localhost
  -sourcedatabase Test -sourceschema dbo -sourcetable TableDiff1 -destinationserve
  r localhost -destinationdatabase Test -destinationschema dbo -destinationtable T
  ableDiff2


Microsoft (R) SQL Server Replication Diff Tool
Copyright (c) 2008 Microsoft Corporation

User-specified agent parameter values:
-sourceserver localhost
-sourcedatabase Test
-sourceschema dbo
-sourcetable TableDiff1
-destinationserver localhost
-destinationdatabase Test
-destinationschema dbo
-destinationtable TableDiff2

Table [Test].[dbo].[TableDiff1] on localhost and Table [Test].[dbo].[TableDiff2]
 on localhost have 2 differences.
Err     TableID
Src. Only       3
Src. Only       4
The requested operation took 0.1573824 seconds.


Next, we create a View that has a WHERE filter to select only the FilterColumn = 1 rows:

GO
CREATE VIEW TableDiff1_Filtered
AS
SELECT TableID, FilterColumn, TableData
FROM TableDiff1
WHERE TableDiff1.FilterColumn = 1;


Now, when we run TableDiff.exe against the view, we get the desired results.  Only a single row is identified as missing from the destination table (the row we added after "replicating" the rows from the source table).


  C:\Program Files\Microsoft SQL Server\110\COM>TableDiff -sourceserver localhost
  -sourcedatabase Test -sourceschema dbo -sourcetable TableDiff1_Filtered -destina
  tionserver localhost -destinationdatabase Test -destinationschema dbo -destinati
  ontable TableDiff2


Microsoft (R) SQL Server Replication Diff Tool
Copyright (c) 2008 Microsoft Corporation

User-specified agent parameter values:
-sourceserver localhost
-sourcedatabase Test
-sourceschema dbo
-sourcetable TableDiff1_Filtered
-destinationserver localhost
-destinationdatabase Test
-destinationschema dbo
-destinationtable TableDiff2

Table [Test].[dbo].[TableDiff1_Filtered] on localhost and Table [Test].[dbo].[Ta
bleDiff2] on localhost have 1 differences.
Err     TableID
Src. Only       4
The requested operation took 0.1220787 seconds.