Will there be consequences overstayed with no special pass?

Hi all,

I'm work in one company in Selangor. My EP category III expired in Oct 2018 and because of some reasons my company haven't renew it, still in process for documents and but not in submit step yet. And i'm not holding any visa to stay. So i consider my condition currently is overstayed already. Even my company tell me to not worry, but i'm so worry because it's 3 months expired already. My questions are:

1. When my company submit documents to renew EP later, that actually it's expired already for 3 months, is there any consequences, like penalty or something that gonna happen? Both for me and company. Since i'm not holding any visa, like special pass, to stay.
2. Is there any additional documents that need to prepare when submit renewal with overstayed condition above?
3. Is there any suggestion what to do while waiting my company to submit for renewal? Is it better to apply special pass or something?

Thank you