The reason for this many rejection (Only flagging) of patterns is due to the spiky beam. When the current stability cut limit is set to 1-sigma deviation to reject beam current ramps, I never expected to have this spikes in the beam.
see Standard Error Flag Effect on Beam Trips/Ramps
I could adjust the stability sigma little bit but that requires further study of this spikes property of the beam. It would be great if anyone willing to give some ideas.