Got it! I added two derived tables to the query to flatten it out. Seemed to do the trick:

select C.MRN,

C.FirstName,

C.LastName,

C.Date_of_Birth,

t.PatientCoPay,

t.AssistancePay as "CoPay Card Assistance",

t.CoPayCardInsurance,

t.CoPay_Policy_Number,

u.AssistancePay as "Commercial Assistance",

u.CommercialInsurance,

u.Commercial_Policy_Number,

C.Date_Filled,

C.Physician

from(

SELECT distinct HR.MRN MRN,

HR.FIRST_NAME FirstName,

HR.LAST_NAME LastName,

CONVERT(VARCHAR(10),HR.DOB, 101) Date_of_Birth ,

CONVERT(VARCHAR(10),lablog.curdate, 101) Date_Filled ,

--patins.policy Policy_Number,

NCPDP.drugname Drug,

--claims.expected AssistancePay ,

--ncpdp.copay Patient_CoPay ,

--patins.payor,

--INSCOMP.ORG Insurance,

hr.physician Physician ,

ncpdp.occ

,CLAIMS.CFK_INVOICES InvoiceNum

FROM INSCOMP

JOIN CLAIMS ON INSCOMP.NO = CLAIMS.CFK_INSCOMP

JOIN HR ON CLAIMS.CFK_HR = HR.[MRN]

JOIN NCPDP ON NCPDP.mrn = hr.mrn

AND NCPDP.BILLNO = claims.CFK_INVOICES

JOIN parts ON parts.name_ = NCPDP.drugname

JOIN patins ON PATINS.CPK_PATINS = claims.CFK_PATINS

JOIN labels ON labels.no = parts.no

JOIN lablog ON lablog.CPK_LABLOG = ncpdp.LABLOGNO

WHERE lablog.curdate BETWEEN '04/01/2015'AND '06/30/2015'

AND [cprsql].dbo.HR.MRN = 003137

AND CFK_INSCOMP <> 99999

AND INSCOMP.DELFLAG= 0

AND CLAIMS.DELFLAG= 0

AND HR.DELFLAG = 0

AND lablog.ndc IN ('61958180101',

'00074309328',

'00004035730',

'00004035239',

'00004036030',

'00004036530',

'00004035009',

'00085435301',

'00085132301',

'00085131601',

'00085127901',

'00085129701',

'00085129702',

'00085137001',

'00085137002',

'00085131602',

'68084017965',

'65862029018',

'65862020768',

'66435010899',

'66435010599',

'66435010699',

'66435010799',

'66435010118',

'66435010216',

'00781204304',

'00781204304',

'00093722758',

'00093722763',

'00093722772',

'00093722777',

'68382026012',

'68382004603',

'00074327156',

'00074328256',

'00074322456')

AND ncpdp.occ = 08

AND exists

(SELECT 1

FROM INSCOMP AS INSCOMP_B

JOIN CLAIMS AS CLAIMS_B ON INSCOMP_B.NO = CLAIMS_B.CFK_INSCOMP

JOIN HR AS HR_B ON CLAIMS_B.CFK_HR = HR_B.[MRN]

JOIN NCPDP AS NCPDP_B ON NCPDP_B.mrn = HR_B.mrn

AND NCPDP_B.BILLNO = CLAIMS_B.CFK_INVOICES

JOIN parts AS parts_B ON parts_B.name_ = NCPDP_B.drugname

JOIN patins AS patins_B ON patins_B.CPK_PATINS = CLAIMS_B.CFK_PATINS

JOIN labels AS labels_B ON labels_B.no = parts_B.no

JOIN lablog AS lablog_B ON lablog_B.CPK_LABLOG = NCPDP_B.LABLOGNO

WHERE INSCOMP_B.org LIKE '%Medtrak%'

AND lablog_B.curdate BETWEEN '04/01/2015'AND '06/30/2015'

AND HR_B.MRN = 003137

AND CLAIMS_B.CFK_INSCOMP <> 99999

AND INSCOMP_B.DELFLAG= 0

AND CLAIMS_B.DELFLAG= 0

AND HR_B.DELFLAG = 0

AND lablog_B.ndc IN ('61958180101', '00074309328', '00004035730', '00004035239', '00004036030', '00004036530', '00004035009', '00085435301', '00085132301', '00085131601', '00085127901', '00085129701', '00085129702', '00085137001', '00085137002', '00085131602', '68084017965', '65862029018', '65862020768', '66435010899', '66435010599', '66435010699', '66435010799', '66435010118', '66435010216', '00781204304', '00781204304', '00093722758', '00093722763', '00093722772', '00093722777', '68382026012', '68382004603', '00074327156', '00074328256', '00074322456')

AND NCPDP_B.occ = 08

AND HR.MRN = HR_B.MRN)

GROUP BY HR.MRN,

HR.[FIRST_NAME],

HR.[LAST_NAME],

CONVERT(VARCHAR(10),HR.DOB, 101) ,

CONVERT(VARCHAR(10),lablog.curdate, 101) ,

patins.policy,

NCPDP.drugname,

claims.expected ,

ncpdp.copay ,

patins.payor,

INSCOMP.ORG,

hr.physician,

patins.rank,

ncpdp.occ

,CLAIMS.CFK_INVOICES

)C

join (

select distinct ncpdp.MRN,ncpdp.BILLNO as BillNum,ncpdp.copay as PatientCoPay, CLAIMS.EXPECTED as AssistancePay, (ncpdp.copay + CLAIMS.EXPECTED) as OriginalCopay,patins.insurance as CoPayCardInsurance,patins.policy as CoPay_Policy_Number

--,*

from NCPDP

join CLAIMS on CFK_INVOICES = ncpdp.BILLNO

join PATINS on PATINS.CPK_PATINS = claims.CFK_PATINS

where patins.PAYOR = 'COPAY CARD'

and OCC = 08

and NCPDP.DELFLAG <> 1

and claims.DELFLAG <> 1

and patins.DELFLAG <> 1

and ncpdp.MRN = 3137

--and ncpdp.BILLNO = 40451

) t on t.mrn = C.MRN and C.InvoiceNum = t.BillNum

join (

select distinct ncpdp.MRN,ncpdp.BILLNO as BillNum,ncpdp.copay as PatientCoPay, CLAIMS.EXPECTED as AssistancePay, (ncpdp.copay + CLAIMS.EXPECTED) as OriginalCopay,patins.insurance as CommercialInsurance,patins.policy as Commercial_Policy_Number

--,*

from NCPDP

join CLAIMS on CFK_INVOICES = ncpdp.BILLNO

join PATINS on PATINS.CPK_PATINS = claims.CFK_PATINS

where patins.PAYOR = 'COMMERCIAL'

and OCC = 08

and NCPDP.DELFLAG <> 1

and claims.DELFLAG <> 1

and patins.DELFLAG <> 1

and ncpdp.MRN = 3137

--and ncpdp.BILLNO = 40451

) u on u.mrn = C.MRN and C.InvoiceNum = u.BillNum