There are a lot of entries in SCN involving your issue 
Have you looked for carefully before posting a question :-?
1. check your configuration in T554S with T-Code SM31 -> finding your counting rule
2. check counting rule in T556C with corresponding ESG and PSG. If the day meets ALL conditions in counting rule, whenever applying Absence in IT2001, it will be deducted Absence Quota in IT2006.
Assuming your Holiday class is 1, just uncheck it in T556C, it will not deduct IT2006 anymore.
Regards!
Woody