Try this :

WITH GroupPatients AS 
    (SELECT MeasurementID, PatientId, Count(*) AS cnt
    FROM PatientMeasurement AS pm
    INNER JOIN Patient p ON pm.PatientID = p.PatientID
    WHERE
        MeasurementId IN ( A ,  B )
    AND
        Recorded <= dateadd(hh, 12, Admitted)
    GROUP BY MeasureMentID, PatientId)

SELECT p.PatientID, Case
    When IsNull(GPA.cnt, 0) > 0 AND IsNull(GPB.cnt, 0) > 0 Then 1
    Else 0
End AS Numerator, 1 AS Denominator
FROM Patient p
LEFT JOIN GroupPatientsA AS GPA ON p.PatientID = GPA.PatientID AND GPA.MeasurementID =  A 
LEFT JOIN GroupPatientsB AS GPB ON p.PatientID = GPB.PatientID AND GPB.MeasurementID =  B 

I ve made one tweak to the business logic too - your spec says Numerator should be one if a patient has both A and B measurements - however, your clause of a.cnt+b.cnt>2 will erroneously return one if either a.cnt or b.cnt are 3 or more and the other is zero.

Another solution can be close to your original attempt using OUTER APPLY:

SELECT  PatientId, CASE WHEN a.cnt+b.cnt>2 THEN 1 ELSE 0 END Numerator, 1 Denominator 
FROM    patient p 
OUTER APPLY ( 
    SELECT      count(*) cnt 
    FROM        PatientMeasurement pm 
    WHERE       MeasurementId= A  
    AND       Recorded <= dateadd(hh, 12, p.Admitted) 
    AND pm.PatientId = p.PatientId
) AS a(cnt)     
OUTER APPLY ( 
    SELECT      count(*) cnt 
    FROM        PatientMeasurement pm 
    WHERE       MeasurementId= B  
    AND       Recorded <= dateadd(hh, 12, p.Admitted) 
    AND pm.PatientId = p.PatientId
) AS b(cnt)

SELECT  p.*, 
        CASE WHEN
        EXISTS
        (
        SELECT  NULL
        FROM    PatientMeasurement pm
        WHERE   pm.PatientID = p.ID
                AND pm.Type =  A 
                AND pm.Recorded <= DATEADD(hh, 12, p.Admitted)
        ) AND EXISTS (
        SELECT  NULL
        FROM    PatientMeasurement pm
        WHERE   pm.PatientID = p.ID
                AND pm.Type =  B 
                AND pm.Recorded <= DATEADD(hh, 12, p.Admitted)
        ) THEN 1 ELSE 0 END
FROM    Patient p

Assuming you are using Sql 2005 or 2008, the entire query can be simplified using some window functions and a pivot:

with pData as
(
    select  count(*) over(partition by PatientId, MeasurementId) as cnt,
            PatientId, MeasurementId
    from    PatientMeasurement pm
    where   MeasurementId in( A , B )
    and     Recorded <= dateadd(hh, 12, Admitted)
)
select  PatientId, coalesce([A],0) as cntA, coalesce([B],0) as cntB,
        case when coalesce([A],0) + coalesce([B],0) > 2 then 1 else 0 end as Numerator,
        1 as Denominator
from    pData
pivot   (max(cnt) for MeasurementId in([A],[B])) pvt

DECLARE @TimeSlot int;
SET @TimeSlot = 12;

WITH 
pt AS (
    SELECT p.PatientID, p.Admitted, m.MeasurementID, m.Recorded,
        CASE 
          WHEN m.Recorded <= dateadd(hh, @TimeSlot, p.Admitted) THEN 1 
          ELSE 0 
        END AS "InTimeSlot"
    FROM Patient AS p
    LEFT JOIN PatientMeasurement AS m ON p.PatientID = m.PatientID
),
cntA AS (
    SELECT PatientID, count(*) AS "A_count"
    FROM pt WHERE MeasurementID= A  AND InTimeSlot = 1
    GROUP BY PatientID
),
cntB AS (
    SELECT PatientID, count(*) AS "B_count"
    FROM pt WHERE MeasurementID= B  AND InTimeSlot = 1
    GROUP BY PatientID
),
cntAB AS (
    SELECT p.PatientID
          ,coalesce(a.A_count, 0) AS "A_cnt"
          ,coalesce(b.B_count, 0) AS "B_cnt"
    FROM Patient as p
    LEFT JOIN  cntA  AS a ON p.PatientID = a.PatientID
    LEFT JOIN  cntB  AS b ON p.PatientID = b.PatientID
),
cntN AS (
    SELECT PatientID,
        CASE WHEN A_cnt > 0 AND B_cnt > 0 THEN 1 ELSE 0 END AS Numerator
    FROM cntAB 
)
SELECT PatientID, Numerator, 1 AS Denominator FROM cntN