The two outer apply s in your query effectively form multiple independent one-to-many joins, which can cause data duplication and inflated aggregated results. For example, if you had 3 matching TransactionTypeid = 5986 rows and 4 matching TransactionTypeid = 5982 rows, the combined joins would yield 12 result rows feeding the group-by. The 5986 rows would be counted 4 times each and the 5982 rows would be counted 3 times each.

The solution is to move the aggregation inside the outer-apply, so that each yields exactly one row of already-aggregated data. (The outer-apply could actually become a cross-apply at that point.)

Try:

SELECT 
        FAT.DateId,
        FAT.EffectiveDateId,
        FAT.TransactionTypeId,
        FAT.Amount,
        FAT.MKey,
        E.[805 Trans],
        E.[805 Amount],
        D.[809 trans],
        D.[809 Amount]
FROM Warehouse.fact.AccountTransaction FAT 
    JOIN warehouse.dim.TransactionType tt 
        ON tt.TransactionTypeId = fat.TransactionTypeId
           AND tt.SrcBaseId = 3
           AND FAT.DateId >= 20221101
           AND tt.TrnCode = 2310
           AND fat.MKey = 1234
    CROSS APPLY (
        select
            count(FAT1.MKey) AS [809 trans],
            sum(FAT1.Amount) AS [809 Amount]
        from Warehouse.fact.AccountTransaction fat1 -- // 809
        where FAT1.MKey = 7341096
           AND FAT1.TransactionTypeid = 5986
           AND FAT1.SrcBaseId = 3
        and CONVERT(datetime, convert(char(8),FAT1.EffectiveDateID)) between CONVERT(datetime, convert(char(8),FAT.EffectiveDateID))  and dateadd(DAY,10,CONVERT(datetime, convert(char(8),FAT.EffectiveDateID)))
        --      group by FAT1.SrcMor97InstId,
        --          FAT1.MKey,
        --          FAT1.Amount
        )
    ) D
    Outer APPLY (
        -- // 805
        select
            count(FAT2.MKey) AS [805 trans],
            sum(FAT1.Amount) AS [805 Amount]
        from Warehouse.fact.AccountTransaction FAT2
        where FAT2.MKey = 7341096
           AND FAT2.TransactionTypeid = 5982
           AND FAT2.SrcBaseId = 3
            and CONVERT(datetime, convert(char(8),FAT2.EffectiveDateID)) between CONVERT(datetime, convert(char(8),FAT.EffectiveDateID))  and dateadd(DAY,10,CONVERT(datetime, convert(char(8),FAT.EffectiveDateID)))
        -- group by 
        --        FAT2.SrcMor97InstId,
        --       FAT2.MKey,
        --       FAT2.amount
    ) E

group by
        FAT.MKey,
        FAT.DateId,
        FAT.EffectiveDateId,
        FAT.TransactionTypeId,
        FAT.Amount

I am unsure what the intended purpose of the inner GROUP BY s. I have tentatively commented them out. It is unusual to see a GROUP BY ...Amount , where that amount is eventually fed into a SUM(Amount) . That can lead to accidental dropping of amounts from the calculation just because they match other amounts.

If the inner group-bys are needed, you can wrap them into a subselect within the cross-apply:

CROSS APPLY (
        SELECT
            count(D.MKey) AS [809 Trans],
            sum(D.amount) AS [809 Amount]
        FROM (
            select FAT1.SrcMor97InstId,FAT1.MKey,FAT1.Amount
            from Warehouse.fact.AccountTransaction fat1 -- // 809
            where FAT1.MKey = 7341096
               AND FAT1.TransactionTypeid = 5986
               AND FAT1.SrcBaseId = 3
               and CONVERT(datetime, convert(char(8),FAT1.EffectiveDateID)) between CONVERT(datetime, convert(char(8),FAT.EffectiveDateID))  and dateadd(DAY,10,CONVERT(datetime, convert(char(8),FAT.EffectiveDateID)))
            group by FAT1.SrcMor97InstId,
                  FAT1.MKey,
                  FAT1.Amount
        ) D
    ) D
    CROSS APPLY (
        SELECT
            count(E.MKey) AS [805 Trans],
            sum(E.amount) AS [805 Amount]
        FROM (
            Select SrcMor97InstId, MKey, FAT2.amount
            from Warehouse.fact.AccountTransaction FAT2
            where FAT2.MKey = 7341096
               AND FAT2.TransactionTypeid = 5982
               AND FAT2.SrcBaseId = 3
               and CONVERT(datetime, convert(char(8),FAT2.EffectiveDateID)) between CONVERT(datetime, convert(char(8),FAT.EffectiveDateID))  and dateadd(DAY,10,CONVERT(datetime, convert(char(8),FAT.EffectiveDateID)))
            group by 
                FAT2.SrcMor97InstId,
                FAT2.MKey,
                FAT2.amount
        ) E
    ) E

I believe you can also combine the two cross-applys by selecting both TransactionTypeid values in the subquery and using conditional aggregation to later separate the values.

CROSS APPLY (
        SELECT
            count(CASE WHEN TransactionTypeid = 5982 THEN D.MKey END) AS [805 Trans],
            sum(CASE WHEN TransactionTypeid = 5982 THEN D.amount END) AS [805 Amount],
            count(CASE WHEN TransactionTypeid = 5986 THEN D.MKey END) AS [809 Trans],
            sum(CASE WHEN TransactionTypeid = 5986 THEN D.amount END) AS [809 Amount]
        FROM (
            select FAT1.TransactionTypeid, FAT1.SrcMor97InstId, FAT1.MKey, FAT1.Amount
            from Warehouse.fact.AccountTransaction FAT1 -- 805/809
            where FAT1.MKey = 7341096
               AND FAT1.TransactionTypeid IN (5982, 5986)
               AND FAT1.SrcBaseId = 3
               and CONVERT(datetime, convert(char(8),FAT1.EffectiveDateID)) between CONVERT(datetime, convert(char(8),FAT.EffectiveDateID))  and dateadd(DAY,10,CONVERT(datetime, convert(char(8),FAT.EffectiveDateID)))
            group by
                  FAT1.TransactionTypeid,
                  FAT1.SrcMor97InstId,
                  FAT1.MKey,
                  FAT1.Amount
        ) D
    ) D