Yes, PF & ESIC shall be in effect on arrears salary. If, in case, last month you got paid less due to any circumstances, and your company paid you for those days in this month, then those days' PF, ESIC (if applicable) shall be attracted on those days' salary, and the employer needs to contribute on the same.
The difference amount of PF & ESIC needs to be paid in the prescribed month along with your respective month's salary. There should be no deductions attracted on Leave Encashment. If you can elaborate on the case, it would lead to a better understanding, and members can also advise you in an appropriate way.
Regards