Grammatically both uses are acceptable. They have slightly different meanings so the correct form to use depends on your context.
If the "incomplete stone removal" can still be considered to be the causative agent for the "recurrent cholangitis" then you should use "It IS".
If however the incomplete stone removal stopped being the reason for the sickness or if perhaps there was some other factor at play then you could use "It WAS".
Our initial diagnosis indicated that it was the incomplete stone removal that caused the recurrent cholangitis. As there was no improvement in the patient's condition after complete removal of the stone residues it became apparent that another factor was involved.