My dad's employer filed a petition for him back in 200 along with the 245-I. The employer did not want to proceed with the petition and everything was put on hold. On the petition it was my dad, mom and sister who was a minor at that time. She is now 27 and I am petitioning my parents, can I petition her at the same time since she was in the first petition a minor?

You can of course petition your parents and siblings if you are a US citizen over 21. Note that sibling is the F4 category which has a wait of about 13 years (19 years for people born in Mexico, 23 years for people born in the Philippines) before a visa number is available. If your sister is unmarried and not born in Mexico, it would be faster for your parent(s) to petition her (as an unmarried over-21 child of a permanent resident, F2B category) than you petitioning her directly.

(Note that you may be thinking of your sister as a derivative beneficiary of your parents. But even if your sister were under 21, she could not be a derivative beneficiary because Immediate Relatives (spouse, parent, or under-21 child of US citizen) can never have derivative beneficiaries.)

The fact that they were beneficiaries of a petition filed before 2001 just means that they are grandfathered for 245(I) purposes and can do Adjustment of Status (if a visa number is available) in the US regardless of entering illegally and/or not being status now. It doesn't have anything to do with who can petition them or how long it takes until a visa number is available.