H1B Visa Dropbox 221G: Wife's visa issued, main applicant visa status still in admin processing after the approval.

Dec 5: Drop Box submitted for me and my wife
Dec 14: Drop box returned while slip 221G with me and my wife passport asking to appear for interview.
Dec 15: Interview at New Delhi with me and my wife and VO said it is approved. VO retained the passport and said to collect from Nehru place in a week.
Dec 18: Wife’s application approved but my case is still in admin processing.
Dec 19: Wife’s passport is ready to pick up, but my case on ceac visa tracker is still in admin processing.

I don’t understand why would Embassy not stamp both the passport together. Does that happen to anybody else too?

It may be related to the way the documents for each visa category are processed at the consulate. Your case might have had some red flags during process, and they would usually do a background check to approve.