we have come across such cases in a factory a few months ago.
The Factory Act actually clearly states that the employee is eligible to payment as soon as he enters the factory and till he leaves, unless you have clear proof that the person was not doing work. It is presumed that he was doing work as long as he was inside the factory.
First step you need to take is to inform the Security not to allow someone into the factory and not let him punch till the shift start time (generally companies allow 15 minutes early sign in for shift change and overlap). Else this problem will continue.
For the rest, you need to involved IR team and decide on it. If he was doing work, then he deserves overtime even if he was not authorised, since that it your internal problem and he can not be penalised for it.
On the other hand, if he did voilate the rules, then you can initiate a domestic enquiry and take the proper steps on it.
Remember that the impact of either action can go far beyond payment to a single employee. Therefore the IR aspect must be carefully studied.