Hi Rohit,
This could be all kinds of config issues, but impossible to say without thoroughly analysing your system.
But one quick and easy check I always do first in this situation, even if the customer says it can't be the case: is there any further record of IT2006 the deductiin is taken from? It could be a duplicate record created accudentialky, a dufferent quota type also configured to take the absencevtype concerned or, most likely,an older record with the deduction date set far enough into the future to cover the absence record concerned.
If this is definitely not the case and you couldn't find a fault in the config, my next step would be to run the update report for one person affected and pick a goid place to start debugging what happens. Painful, but that would eventually bring the truth into daylight.
Iid luck!
Scen