Unfortunately, there is no facility to recover CIS tax through the CT600.
CIS tax is an employment tax that's deducted from a limited company's gross income and therefore forms part of the PAYE system. Unfortunately, HMRCs systems do not synchronise information and therefore the required entries would need to be kept separate.
This was previously submitted via a P35 (Employer's Annual Return). This form ceased to exist from 06/04/2013 and now the information is captured via the usual Real Time Information (RTI) payroll data which is submitted. This would usually be included within the Full Payment Submission (FPS) and the Employer Payment Summary (EPS).
Usually a refund is issued mid-summer, rather than a deduction when Corporation Tax is due.