Without judgement, please, I need help. I am in Israel at the moment and have been here for longer than 90 days, surpassing my allowed 90 day allowance. Am I going to get in trouble when I go to get my visa? I am a student and I have been here almost four months now... I am afraid to go get my visa because I'm overdue. Will they kick me out? Will I be okay? I don't know how much they enforce the 90 day rule.
This page gives some information on Israel visas.
By comparison with other countries, Israel seems to be fairly laid-back about overstays.
Note that overstaying your allotted time elicits a fine of 135NIS per month – this can be sorted out at Ministry of the Interior offices or Ben-Gurion airport, but not at land borders. Travellers who overstay by just a few days report no hassles or fines.
However this doesn't necessarily mean it won't impact your actual visa. If you overstayed one time, they might think you will overstay again. I can't think of any reason why waiting would make this better - if your visa is ready for collection, go get it sorted out now.